Yeah, I've wondered the same thing. Of course, it wouldn't be "to spec", but it would work with 99% of the boards out there today, and it would allow much more efficient cooling. It's that final 1% compatibility issue that kind of puts the nail into the coffin though.
Additionally, my current case, as do many other mid-tower ATX cases, has a fan port above the ATX I/O bracket. I currently have a 80mm temp-controlled fan mounted there, pointing INWARDS, with the thermal sensor connected to my AGP card's GPU heatsink assembly. (Radeon 9200, no fan, but it doesn't OC too well either because of heat.) I'm not really sure how much the fan helps (was working on PC last night, noticed I had a couple of spare fans, so I just threw it in there). If the GPU/heatsink was on top of the AGP card, then that intake fan would blow cool air directly over both it, and the CPU HSF assembly, possibly also the DIMMs located behind the CPU HSF from the view of the fan.