MicroATX boards are physically smaller than standard ATX boards, hence they generally also have a smaller feature set then standard size boards. As mentioned by the other poster though, it doesn't make a large amount of difference. Especally if you're just using the machine for basic tasks and a but of gaming and not some super strong gaming setup where you might want to have more expansion slots and better cooling.
Granted, i am not 100% sure if the case can fit standard ATX size boards as even on Sony's website it doesn't mention what size boards it fits.
Here's a list of a few MATX boards on Amazon: http://www.amazon.com/s/ref=nb_sb_ss_sc_4_8?url=search-alias%3Daps&field-keywords=micro+atx+motherboard&sprefix=microatx%2Caps%2C200