Historicly (from almost begining), there have been diference betwen clans and omni.
Clans were for more xp, Omni for better stuff. There were many stuff (especialy buffing ones and so) with were exclusivly for omnis.
I guess Clan whining and so did make that almost everything has clan/hacked version curently. So that it doesnt matter what you chose. With feels wrong. There must be diferences in gear, maybe even buffs/nanos. They both are big factions.
(As a humor note, it all migh have been hapening because ARK and GM are Clan :P)
(Sorry about my english, not my native, so might be few mistakes in my grammar)