I'd like to see more games based on licensed properties that don't suck. The main problem I see is that a lot of them (Serenity, Wheel of Time, Babylon 5) adhere to the show/book/movie that the only kinds of PCs that can be made are mix and match clones of canon characters and the only settings given any description are those from the show. Sometimes this outright cripples the system, sometimes it just makes it so that the group has to do a hell of a lot more work. Either way, there's such a huge opportunity to expand on things with an RPG, but it rarely gets taken advantage of, either because of the nature of the license or because of laziness. And a lot of the other licensed properties just outright get turned into shitty games.
Aside from that I'd like to see games based on Ghost in the Shell and Fallout, at the very least. The Empire of Man series by David Weber and John Ringo might be fun to play around in. Same with the Honor Harrington series. I'd like to see a good "classic" Final Fantasy game, as well as a good Diablo game. Yes, I know that both could probably be modeled with some flavor of D&D, but I'd like to see something more specific. Diablo in particular would benefit from the additional detail to the setting that an RPG could provide. I'd like to see a Star Ocean and/or Tales RPG. Front Mission could be a really fun game too, rather Battletech/Mechwarrior-esque.
3. The Dresden Files, of course
This is actually being worked on. It's supposed to use the Fate system (a la Spirit of the Century).