ATX or mATX... I wrestled with this debate for quite some time.
I knew going in that I wanted something physically smaller than the Mac Pro that I was coming from. I looked at the PCI-e cards, I had in my Mac Pro...
1. Graphics card
2. SATA 3 card
3. SSUBX to PCI-e adaptor
4. USB 3
Not counting the video card, everything else was built in to modern motherboards. Even USB 3.1 is built in now. The only thing that I would really have to add would be Wifi/Bluetooth (I wish manufacturers would incorporate M.2 or mini PCI-e slots for these in motherboards other than ITX ones.)
I also thought to myself,
how many PC users actually have all their PCI-e slots filled. The only situation that I could imagine was users with multiple video cards which I would never do.
Currently, I have (1) video card, (2) 10GbE card, and (3) Wifi/Bluetooth. The 10GbE card is more of a luxury than a necessity for me and I could replace it if the need ever arose.
I must add that the extra amount of desk space that my case gives me over the Mac Pro's case is huge. Even pictures can't fully do it justice. By my totally unscientific guesstimate, I would say it's about a 40% reduction in total volume. (I'm sure you can appreciate this since you have a similar case for your Gene.) This is something that affects me everyday. Until I have another PCI-e card that I want to install, it's a non issue for me.
Sorry for the long winded reply.
Edit:
Here are some pictures to try and illustrate the amount of desk space saved with an mATX vs a Mac Pro. I included side-by-side shots with an HP Elite 8300
Small Form Factor to give additional perspective.