The Extreme 4 ATX is better for overclocking, connectivity, probably a little more reliable, and has better connectivity IIRC (I'd have to check to be more sure). It probably also has somewhat higher power consumption, but a system with a 7970 or otherwise high-end card is probably going to drown out that difference with the graphics and CPU.
However, the Extreme 4 MicroATX versus the Pro4 ATX is a somewhat different deal... Why not get the Extreme 4 ATX? At least in the USA, it can currently be bought even cheaper than the Pro4 ATX and is a fairly high-end board despite it's price. It can hang with most much more expensive boards in the $150-200 range in many respects.