Despite what some people say, I'd still like to see a classless system. Not necessarily a system with no classes, but the ability to be more flexible with character creation would be very valuable. Sure, you can still be a fighter. But wouldn't it be cool if you could, right off the bat, play a thief that can go ethereal, and the system assures you is more or less balanced?
I also like the idea of a freeform spell system. Again, not a replacement for the spells we already have, but an additional layer of functionality that allows nearly any spell effect imaginable to be created.
Then again, I'm just weird. That, and my homebrew system does all this already, so I'm prejudiced. (It doesn't run nearly as fast as D&D, tho.)