It can be done but it costs more than a ATX or u-ATX and there are serious thermal issues.
The only thing that Mini-ITX builds cost more in is with cases, since I haven't found a decent $40 case. But otherwise, all of the other parts on my current builds BOM is more or less the same as a uATX or ATX build. Heck, the motherboard I bought, the ASRock Z87E-ITX, costs about as much as the Gigabyte GA-Z68XP-UD3 ATX board I bought for my last build, and I would argue the Z87E-ITX has more features (more 6Gbps ports, USB3.0 ports, Wireless 802.11ac included).
As for serious thermal issues, the Prodigy hasn't given me any issues at least on the GPU side (I'm cheating with a water cooler). Besides, they cramp 150W hardware in gaming consoles with less breathing room than most ITX cases.
Future expansion is pretty much non-existent as well.
My last build has taught me one thing: gaming computers rarely get expansion anyway. The only other expansion card I added were sound cards, which onboard sound has reached a point where having a sound card seems kind of silly (mostly because the only reason why gamers would need one died a long time ago). I also don't find SLI or Crossfire worthwhile. Yes I've done it, but the additional requirements plus the extra waste generated I don't find worth while anymore.
The only thing I see that's lacking is two extra RAM slots and fewer SATA ports. But 8GB (in a 2x4GB configuration) is still plenty for gaming builds and the most SATA devices I installed were 4 and I've reduced that to 2.
Then again I'm the kind of person who builds completely new systems every few years. Either way though, tailor the build to your needs.