when purchasing a mobo, you need to ask yourself what will you do with it in the future. what mobo perks do you need. how many sata 6x ports do you need(dependant on # of hdd/ssd you will have). how many spare pci slots do you need. how many pci express you need, single, dual, triple or quad and at what speed when in sli/crossfire. also choice on overclocking potential as well affects the board. In the end really, it all adds up to what you need on your mobo.
edit: then you throw in other kinks like # of ram slots, ram frequency support, # of mobo fan pins(rest of the fans will have to connect to the psu, and depending on where its located, wires can get tricky to manage). Heat spreaders on parts etc