I'd like to see a shift to putting the AGP card on the bottom of the motherboard, and having a dedicated fan pulling air across it and straight out the back. Also, how about a light inside that you can flick on when you're trying to see the jumpers (for those of us with jumpers to deal with).
An innovative feature would be drive bays that are spaced away from eachother a little, and a fan/duct system that feeds air inbetween the drives, possibly with slide-in baffles to limit the airflow to the areas with drives in them.
Ok, here's another one: instead of having screws to hold the cards into their slots, how about a flip-down bar to keep them in place?
The other thing is noise. If someone put a serious effort into a mainstream case with noiseproofing... I mean, one that you can put loud CPU fans into (YS Tech HO 60mm) and still have a pretty quiet box.