Hmmm, thats a big question to ask and I doubt I'll think of'em all in one post. Not without a
TL;DR wall of text anyway.
So instead I'll just throw one idea out there that no MMORPG to date has done it (although some are trying). Being able to play in the world/game in multiple ways, and what I mean by that is this. Let's say for example there was a Battletech: Mechwarrior MMORPG. If there was, I'd want to be able to pilot 'mechs, yeah that'd be cool... but; I'd also want to be able to hop into an aerospace fighter or hitup some space combat. I'd want to be able to do "people" missions as well, perhaps FPS style to shake things up. All these different ways and genre's of playing a game that melded into a single shared MMORPG experience. Everyone in the same "shard" too.
Bonus pts if it had multiple PvP factions. PvP warzones of fighting and capturing systems back and forth. All that but not free-for all pvp everywhere. I like areas that are pve, and others that are pvp. So when I feel like one or the other I can engage in that without having to bother with it when I don't.
Also, and this is something I really miss about my first MMORPG, but regular monthly content updates. It was a staple feature of Asheron's Call. Every month you'd have some new things to do. Seasonal flair sure but the story of the world also developed a little more each month. The world even changed at times, drastically. A fortnight before there would be teasers, hints at what was coming. They wouldn't be listed out in patch notes though, you'd have to search the world to find them (there'd be clues, from the teasers and also the npc town cryers). People would race to find them out and then report them to their favorite websites. It really brought the community together.