I'd make a Shadowrun MMO

Novel to follow
--Character creation--
Would be much like the table-top, but with some options/changes to make life easy on the newb.
No classes, no levels. Just races, each with some advantages and disadvantages. It'd be a skill-based game. The closest thing to level is in magic initiation. I'd also use the point-buy setup from the game. Give the ability to allocate those points however you wanted between stats, skills, spells, resources, and even your race. If possible, I'd add the edges and flaws to help further customize the charaters.
And there'd be archetype templates you could choose from and then modify if you wanted. These templates would auto-allocate all the points and give some brief descriptions of the character setup and playstyle. And it'd have another set of templates for getting gear. Ones to match the character templates, as well as a ton of little "packages" of various costs. Like one might have a Gun, armor vest, holster, clips, and ammo as a basic kit.
Everything in character generation would have an extra little window with in-game descriptions and also some stat descriptions, and a little blurb of advice. The advice would be given based on the starting archetype/stats/skills you picked. So for a street sam it'd be reccommending against buying magic talismans, while a magic-capable character would be advised of the penalties in taking cyber. Things like that to help the newb avoid accidentally gimping himself through ignorance.
Oh, and plenty of cosmetic options ^_^
--Character Advancement--
Comes in the form of Good Karma (ie: experience) and Nuyen (money). And I'd add some ways to exchange one for the other to a small degree. After all, cyber sams need more money for new enhancements, while mages need more karma to perfect thier spells. It'd take time to do the change though, so not simple for someone to ebay the money and get mega karma. And the change would take place over time, wether logged in or not.
Things would actually need some time to train or build-up, too. To advance a skill, you can choose to learn it by yourself, or from an instructor (which costs extra money). Then you can either spend time in-game learning it actively (like going to the shooting range to practice your pistol skill), or just let it go offline and your character will be studying while you attend to Real Life. Likewise for implants. Go to a doc to undergo surgery, or log out and your character will do it while you're off-line. This may seem a bit odd, but I think it'd help keep immersion going while not being a big inconvenience for the players.
--Content--
In game, you'd have the entire Seattle sprawl for the game. From the apacolyptic wastes of the Barrens to the hip Downtown area. Later content expansions can add more regions like the NAN, or the Elven nation. Tons of expansion possibilities. And there's already a lot of material to work with, but without the stifling strickness of settings like the Star Wars universe.
You'd have a contact system a little bit like City of Heros. The fixer sets you up with Johnsons who in turn have job offers for you or your team. You'd be able to try to negotiate with them, too! And in your NPC interaction, you'd have both your character's negotiation type skills, and a set of dialog options that combine, along with your charisma, to determine thier responses. Kinda like Fallout. Oh and your race can affect it too. The Humanis Policlub Johnson's not going to like talking to a troll, after all.
There'd be some static missions to do, a whole slew of pre-generated ones to do like CoH has, and also a ton of on-the-spot generated ones like AO had. Generated ones can be the generic runs like Steal some data, exctract an employee, yadda yadda.
Rewards would be more flexible, too. And you'd be informed upfront what your choices were (modified by any negotiations). Like an Ares Macrotech Johnson might offer good pay, but also have a selection of guns you could take as part of your payment. And generated missions would try to match the generated rewards to what you could actually use, so no troll-size motorbike for a dwarf.
And for heaven's sake, no static spawn points. Cetain areas would be prone to spawn a certain range of critters (like devil rats in the sewers, but not in the corporate enclave), but no static camp spots.
And instances! Wherever possible missions will be instanced for the group completing it, and whoever they decide to invite.
--Economy--
All sorts of options here for ye olde buy/sell.
*Simple in-game bulliten boards on the Matrix players can post things to, like an in-game ebay.
*buying and selling things through your fixers, which would be based on a combination of store price and current average player-auction prices.
*The actual stores themselves, for things legal.
*Pawn shops for some quick cash on about anything, but it'd pay less then just about anywhere.
*Delivery systems! Send items around to other players easy as pie! Once again, your fixer can do this for illegal goods.
And it can have all the transactions happen while you're offline if you want to sell.
Every economy will need a money sink, and there are some in this game too. Just about anything can degrade and break. Mind you, it's not gone, but it'll cost to get it fixed, and will likely need some skills to do it. Again, if you lack the skill, find a PC to do it, or pay a big fee and have an NPC do it.
There are other costs, too. Like ammo for a gun, replacement grenades, materials for summoning an elemental, and so on.
--Crafting--
Everything has a craft skill, and everything can be made, provided you have the tools for it. From vehicles to spells to guns and armor. If you have the skill, the knowledge, and the tools, you can do it. Of course, a lot of things may require more tools then players tend to get thier hands on, like a factory production line for a car. even if the facilities aren't available, it will be craftable for future expansion, and also to aid in player customization.
Lots of things that can be modifed, too. Like adding burstfire to your heavy pistol, or a supercharger to your car. Or a nice new dikote to your cyber-spur.
Lots of this can also be done for you by NPCs, for a hefty fee, and if they like/trust you.
--Play Environments--
I'd cover as much as possible. And some things I'd even have some fun customization for the players. Deckers, for instance, could get a reality filter for the deck and the game would display whatever textures they might want for things in the matrix. Even have a couple ready-made options for folks without the desire to make thier own. Mages could chose to customize what thier elementals look like, etc.
The mages would have the astral to use. Float around and even fight in this world of thought.
And then the good old mundane world for everyone.
--PvP--
I'd like to make it all-out PvP. But the NPCs would be rather involved as well. If you start a fight on the street in downtown, expect Lone Star to intervene. Out in the Barrens? No one is likely to care.
People could put a bounty on your head and then Bounty Hunter NPCs would start coming after you. Or if you've gotten a big enough police record (like by murdering other players), then Lone Star will start hunting you down, too. Tick off any faction enough, actually, and they may also put a price on your head for a while.
I'd also add some extra options, like a dueling ring, where players can step in and duke it out without outside intervention or the normal penalties of killing each other. And there'd be an actual ladder associated with it, too, for anyone that wanted to climb the ranks. Ladder matches could even accept items in a strongbox for the winner of the fight to claim.
--Death--
This is always a tricky part to me. Make it still be fun, but also a deterrant to being suicidal. Well, I do have an idea. See, in the original game, every so many Good Karma you get (exp) you got a single point of "Karma". This Karma could be used to influence rolls, or burned to help drastically. It could also be dumped entirely for a "Hand of God" that would save your character. So here's the idea:
As you accumulate Karma, the random number generator rolling your dice starts giving you small bonuses on your rolls. You succeed a little more often, basically, mostly focused on helping you avoid catastrophic failure. When you die, you burn some of that karma. The Good Karma (exp) is still there, but the bonus from Karma is reduced. You then respawn in your home. This is a choice, mind you. You can also wait for a player to try to revive you with some medtec skills (at reduced karma loss, depending on skill). You could also spend the money on a Doc Wagon contract, which respawns you in a hospital instead with a reduced amount of karma loss.
If you have no Karma to loose when you die, then one of two things happens depending on your total Good Karma (exp). Before a certain point, you'd be considered a newbie character and just sent home with no further penalty. Above that, it will give a Karma Debt. In essence a penalty to your rolls making you fail more often/spectacularly. That could be paid off with nuyen, by earning more Karma, or by just logging out for a while.
So in every case, you can still gain exp normally, still keep your gear, and your biggest possible obstacle will be travelling back. Meanwhile, the careful player can gradually build a decent bonus (it'd *have* to be capped).
--Factions--
Some was already covered, but I'll add in Factions and Reputation here. What you do will follow you throughout your virtual career. The difference is that you could actually get the chance to join them here. If you manage to join, then you gain access to a lot that factions special goodies, missions, etc. You also get an emblem you can display that you're part of that faction. Of course, if you betray a faction, you can expect some pretty harsh punishments from them if they get thier hands on you. So choose wisely. It can also affect Housing opportunities for yourself, your Team, or your Guild.
--Crime and Punishment--
And hey, what happens when the Star is after you? Not everyone is just out to kill you, after all. I'd add a jail system. If you got caught, you could try to bribe/fast-talk/mind-control the officers arresting you to let you go, or they could haul you in. Then you'd get a police record entry, and depending on what they busted you for maybe bail and walk, or try to break out (sneakily or violently). Or call a buddy NPC and have them get you out (at a loss of face with the NPC/faction). PCs could bail you, too. Or you could just decide to sit in the tank for a few hours (which would go on while logged out, too)
The point is that getting busted should be something to avoid. But if it happens, there should be some entertaining options, and always a way out for the poor broke friendless skill deprived guy.
--Where does it hurt?--
Ahh the old fashion Hit Points ideal. Not here. Everyone has the same basic survival. 1 bar of health, and 1 bar of stun. Both are equal across characters, and both are constant throught the game.
It's how those get hurt that determine the "tanks" out there. A character's stats and some other abilities will allow them to mitigate a certain amount of damage, which can vary for each hit. Armor and the like makes that go more in the character's favor.
The stun bar is damaged by non-lethal attacks like stunguns or fists. When it runs out, you pass out for a bit. Various enhancements can help with this. Once it's gone, those attacks will start hurting your health.
Magic does not use any sort of mana. Rather, it will drain your stun bar. Higher skill and certain attributes can help mitigate this, even to the point of no drain at all.
As either bar goes down, your character starts having trouble. They get penalties piled up on their "dice rolls". No more of the character at 1 hp being every bit as nasty on the attack as the character at full health. On the upside, this also applies to NPCs. This alone could radically change the current method of PvE in MMOs that always focuses on one at a time.
Stun bar naturally regains over time if you're not actively doing much, and recovers very quickly while resting. You are easier to hit while resting though and your combat pool has a lesser effect (see next section for pools)
Health has a lot of ways to heal. From first aid / Biotech skills to medical treatment, to just good old fashioned rest. It does not, however, recover nearly as quickly as Stun with just rest. And, as a side note, going home would restore your health and stun both.
--the Pools--
Combat Pool and Spell Pool.
Combat pool is a slider that adjusts how much effort you put into attack and how much for defense. More attack means you hit more often and likely do more damage, while defense helps you with dodging and absorbing incoming attacks.
Spell pool has 3 bars to allocate it on. 1 for attack with obvious results. 1 for Drain, which helps reduce the Stun bar hits from spell-casting. And 1 for Magical Defense which helps negate incoming spells against you and, optionally, your party.
--Guilds, Groups, and Teams--
Ahh, the multiplayer part. Finally, heh.
Groups of runners get better assignments. More lucrative offers will come for larger groups. And by that, I mean even after the value is divided among the PCs, each one still gets more per mission then they would solo. But, they'd also be harder to complete.
Teams would be a more permenant group. Once setup, the team as a whole can start to build a reputation. The team can get special contacts that only deal with groups, and only offer higher-stakes jobs. The team can also invest together to buy equipment, so they could easily pitch in for a vehicle or whatever. And thier reputation as a team will affect how other NPCs treat them, as an extra factor beyond just individual reputations.
Guilds are the next step up. These are the rare big boys. the runners that hit the big time. A guild builds off a team, and can start managing things on it's own. It can have it's own base of operations, which can include a lot of the hard-to-get crafting facilities. It could even hire it's own fixer to handle buying/selling of guild goods, or handing out guild bounties or missions. They could also hire NPC guards, from the lowly neighborhood gangs to the top-notch private security firms. Guilds can also setup in-house appartments for members.
There are, of course, a limited number places a guild can own. So there's going to be some fighting over them >:} Guilds can duke it out for control of these facilities. Different ones are fought over in different ways. The rougher parts of town have a knock-down drag-out brawl for control. But that's just not going to fly in Downtown. There it's a financial war of bidding to see who will get the contract for the place. Others will have virtual battles on the matrix to gain a hold of it. Some will require appeasing the spirits of the land it's on. And others will be faction-owned and offered to the guilds with the best reputation with that faction. Still others will hold a unique contest appropriate to the facility (like an across-town race for control of a vehicle garage).
--Player Housing--
I've a love-hate with this in most games. I love having it, hate the typical pain of maintaining it. So here's what I'd do:
Players can have appartments. These are instanced rooms/suites inside various buildings across town. They'd offer a lot of nice little bonuses. One already mentioned was full healing. Another is some storage ability. This is especially important since a character themselves can't carry just TONS of stuff. You could setup crafting labs in an apprtment also to do more advanced work. And you'd recieve a bonus on how quickly/easily you repair or refit various things. Like recharging the batteries on your shock-gloves.
You can decorate it, too. And yes, what you decorate with has more effects. Containers give more storage. Work areas make the matching skills easier. Comfort items help off-line skill progression go faster (easier to learn while relaxed). And some others are for fun, like a stereo would let you play music from the game or from a local mp3 folder. And, it's also just nice to have a place to sit when you invite friends over.
And yes, you'll be able to let other people into your appartment. By name, Team, or Guild you could restrict / grant access, or make it entirely public or private if you like. With a second permission set on being able to modify anything in it.
Everyone starts with a basic appartment in a ratty part of town. The place has a basic rent that is assumed to be paid by your character already. No maintenance needed. If you never want fancier, you're set.
Nicer places cost some money to upgrade to. When you get one, you have a couple options. You can pay a weekly (real time) rent which is auto-pulled form your account, or you can pay a much larger sum to just have it permenantly (you invested and pay the rent off the interest or somesuch). If you missed rent payments, rather then getting the boot, it'd go into debt. And while in debt, the appartment's bonuses (except healing) all act at progressively smaller percentage of normal capacity as you go deeper in debt, to a minimum of 10%. You could pay up, or downgrade to something affordable at your leasure.
--Pets--
Lots of types of "pets" in the game. Riggers could have drones, for instance, mages summon elementals, shamans call spirits, and deckers have utility programs in the matrix. And yes, if you have the skills / gear / magic required, you can have them all. At once. Of course, trying to control all that would be rather difficult
In addition, the awakened (magical) characters can also try to get a permenant pet called an Ally Spirit. The difference is that this pet costs Good Karma (exp). And has it's own faction standing with you. Lots of neat things they can do, like help with drain, or even fight/cast on thier own. You can also take control of them directly. But if you treat em rough, they won't like you. And if you get knocked out, and they don't like you, they can try to get free and then bye-bye good karma investment. And if they REALLY don't like you, they'll not only go free, but attack you. So be nice to your little buddy, mkay?
--GM events!--
In addition to the standard stuff to do, and whatever inter-Team and inter-Guild conflicts arise, there's got to be some GM action! I'd be trying to keep the number of servers down to as few as possible. Then I'd have a devoted GM team setup seperate from the in-game support staff that most GMs act as now. This new staff would just run events for players. And this is another area where character repuation comes into play.
See, they'd have access to the database to check on reputations. Then they'd run some of the events to involve large teams and guilds in the plot. Like if a Guild is in good with Lone Star, they could be contacted by a GM-played officer to help out. And always the plot moves onward with at least 1 story-event a month, prefferably 2-4. And they'd be at varying time of day to help include more people.
Also, I'd have a dynamic mission system in the game. It's already been done before, so I'll do it here. Allow GMs to setup various missions via NPCs that will last for a limited amount of time. This also has the bonus of letting them make more content on a lower budget
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If I think of more, I'll add it later =)