Reliability of Minecraft and mods
But the problem truely lies with Java, it's an inefficent programme to make a full on sandbox game, it's not an ideal choice, Minecraft itself, as notch has admitted is not the best written, it also does not truely allow modding.
Mods are a sort of Hack, and bot h Bukkit and Forge are almost 3rd party fixes.
The pipes are great and while thre is limited system issues, The rendering of a single item in the pipe I find effects my server or system very minimally, the problem comes in when items are left on the ground, whether they are from pipes, TNT, or mining, if items fall onto the ground then thats when things get lageriffic for me.
and sadly thats a minecraft issue not buildcraft.
The other limitation is the way the chunks are handled, and of course how the server works. Remember that minecraft has been developed as a single player, Mojong then hacked in a multiplayer component. The thing is that the server side of things is horridly written and is just a hacked and heavily modded single player version. this results in errors, hence the joining of Mojong and Bukkit, they are working on rewriting all the code to make not only modding better, but to make the memory leaks a thing of the past and improve general system performance.
if you want to see what Minecraft can be like, Minecraft for Xbox is stable, stream lined and beautiful, however thats a complete rewrite non java based game. The mods sadly are sometimes better than Mojong at the programming, but they are doing the best they can, with what they have.