I personaly like uATX cases and motherboards. nobody (outside some servers) needs all the space provided by a full ATX any more, unless your SLI/Crossfiring it (and there was at least one SLI mother board built in AXT), and many consider that a waste of money. if your space is limited, and at college it probably will be, uATX is nice to have.
I know what your saying about strick notebook policies. I'm looking to go back, and one of the schools I'm looking at pretty much requires a newer MacBook Pro, and a seperate backup HDD, and a load of high end software. so tack on about $3000 to the already high tuition and the cost of relocating.
there are decent uATX cases out there, but even the good often limit your CPU cooler options. with my Ultra Microfly ( a cube uATX case, similar to some of the Aspires) I upgraded my cooling to a higher end OEM cooler. In my case it was an Opteron 165 cooler on my 65nm dual core. Basicly I got 4 heatpipes and copper fins with a decent fan vs. extruded aluminum and a crap fan. Given the heat output of some of Intel Core2 duals and quads I'm guessing thier coolers are pretty good. look on ebay. given that latly CPU have been getting more efficient, you might be able to carry over the improved stock heatsink to you next build.
Another more extreme option is water cooling. this will work great for you if your willing to put the radiator outside of the case. the water cooling fixtures can be carried over to you next system
if you need more air in your case, you can always just cut holes and add ducts and/or fans. you dont even need more holes, just more fans inside the case will sometimes help with cooling.
the other option is just get a higher flow full sized ATX case and an aftermarket cooler. both should be able carry over to you next build. If you like glowing alien looking boxes with enough fans to require a bigger PSU, then this is the way to go. I personaly like a rather unobtrusive clean small box thats easy to ignore and kicks out almost no light when I'm trying to sleep. When I was robbed recently, they left the computer, but took the screen, so small and unobtrusive has its benifits.
you may be able for find a low end uATX motherboard that has PCIe, DDR1 and suport for your CPU, if all your after is a new graphics card.
personaly I'd say mod you case or get a new one, and upgrade cooling.
if you gat a new case, save to box for the move.