Well you wouldn't want to fit a full size ATX board into a MATX either! Not unless want to snap the board in two!
But you do have to plan, not only for motherboard size, but case layout ie slimline (can't accept multiple cards) tower, depth of case (can cause problems with PSU and drives) PSU fit, optical drives, ability to add hard drives easily, number of hard drive slots, accesilability of components (MATX are cramped compared to full towers) cooling performance, and cooling of hard drives.
I personally would only use full towers, even in a simpler full ATX board system. Just easier to change stuff and adjust things like jumpers/dip switches. Had MATX, midi tower and full tower. Currently use Silverstone TJ-08 MATX micro tower for the HTPC and Stacker 810 for gaming rig.