M-ATX:
+more options for just about everything over the other form factor, period, making it more versatile/flexible.
-some cases are too big to be considered M-ATX; they're ATX.
-it's larger than M-ITX.
M-ITX:
+smaller and more compact than M-ATX.
-Part options are fewer, unfortunately, and it looks to be getting smaller, as more and more manufacturers have slowly backed away from the mini market; demand is low, and so it's considered niche.
If you choose to go with M-ITX, make sure you have thought over what all you want to do with the build, or some 'oopsies' you may come across later might not be remedied without leaving the tiny form factor.