Speaking of pirates, and this is wishful thinking of the preteen anime fanboy variety, I'd love to see a One Piece-based MMORPG. Its already got one of the most established, full-fledged worlds in anime land and it has a GREAT theme to play off of.
Character customization would be rockin'. Considering Oda's artstyle and tendency to make just about every character look unique, I'd imagine a character creation system that exceeds City of Heroes and allows for some pretty robust options for character shapes/sizes.
Beyond that, there would be all the pre-requisite weapons/armor etc. stuff. I'm not sure how Devil Fruits would be handled, though. There would need to be a fair number of them, but only one of each type. This might mean that certain people WOULD get an advantage over others, so I don't really know how they could balance a game like this. Unless they changed continuity and made multiple copies of Devil Fruits and made them available to everybody (a la the powers and skills in CoH).
Of course, there's also the fun of forming a pirate crew and sailing around the four seas and when you get strong enough, you can enter the Grand Line with all the higher level areas.
You could also elect to play as pirates or Navy, which would set up interesting conflicts, and certain strong pirate characters could be elected to Shichibukai position. The Navy would naturally have a heirarchy.
Just a pipe dream, though.

It'd be cool, but all the 12-yr-olds would ruin it.