I've built 7 MATX systems and 3 ATX systems for my friends in 2009, except the few missing PCI slots, there's no difference in term of performance or cooling
the reason why people think MATX is crippled is because the market is flooded with low-end MATX boards. You better check these out...
http://www.evga.com/articles/00487/
http://www.techspot.com/review/154-asus-rampage-2-gene/
http://www.dfi.com.tw/portal/CM/cmpr...rmal&mode=view