Note: I'm not a big ESO lore fanboy. I care more about gameplay. That said...
Imperials being able to join any alliance doesn't bother me - you can make a case that they're "above all that" except where individuals decide to throw in their lot with one alliance or another. So to me, no big deal.
The thing that bugs me a little, though, is the regular pre-order bonus, the "any race can be part of any alliance." Seems like this would be much more of a bastardization of the game than letting Imperials in. I mean, the whole AvAvA aspect of the game was, I thought, predicated on the fact that these guys joined with those other guys and those third guys against the evil <insert enemy races here>. So now, to all of a sudden say "well, yeah, Ebonhart alliance hates Bretons, but all these Bretons joining, well they're defectors who've seen the error of their ways." I could see this aspect tearing a lot of the cohesiveness out of the alliances. Take Ebonhart for example: they've got the Nords, the Dunmer, and the Argonian. I could have envisioned it being easy to peer over the battlefield and see your alliance - Nords charging in, Dunmer spinning magic, Argonians here and there - they're all distinctive. Now though, mix in all the other races and ... it seems mess.
I suppose at some level I don't think this is game-breaking, and I don't think this will cause the game to go F2P, but it sort of saddens me because if feels like a game design change for economic reasons. Think how different WoW would have felt if pre-orders could create Orcs on the Alliance side ... that'd be crazy!