The main problem I had with my last build (mATX) was finding a mATX case (that is, not as tall as a ATX midi-tower) that could also host a decently large cooler.
There's no reason you can't put a mATX board in a mid (or even full) tower, unless you're trying to fit the case into a desk, entertainment center, or other space-constrained area. The motherboard mounting holes and rear panel cutouts are still compatible.
On the counterpoint I went mATX and now think I should've gotten regular ATX instead. I bought a 30in LCD screen after computer build and a single videocard is barely adequate to run it in games.
Yes, SLI is the single biggest reason to avoid mATX. If you think you might ever want to run two video cards, go full ATX.
I've never used SLI, and have no plans to do so. So mATX is fine by me.
If the world isn't making sense to you, you're either drinking too much or not drinking enough.