This probably would require reworking of bunch of story quests, so I don't expect it to happen any time soon if at all, but here we go anyway.
Why I can't be a Warborn that decided to ally himself with Nuia (because for example they've decided that he/she despises Harani so much for what they did to him/her that he/she decides to live as far away from Harani as possible and change the faction because of that) or a Nuian who decided to abandon their goddess and become part of Harania? There are a couple MMOs with factions but either allow you to decide which one to be a part of independently of the race chosen or allow you to change the faction later on. Would love such thing to be a part of ArcheAge as this would make sandbox element even stronger because really, there's no way every member of a given society agrees with politics of said society.