Well, I don't think being Jinchuuriki would affect Sasuke somehow, since he doesn't care for what the villagers think of him. Does he still have sharingan in your AU? If yes, for him nothing would change. If not, I'm affraid he'd commit suicide with all the problems he'll have alltogether.
As for Naruto, well, if his eyes would be like Nagato's (I mean trasplanted), I think he'd just be stronger since the very beginning, but nothing would change significantly. If he had Uchiha DNA, I think it would make him more conflicted due to Sharingan's mind affecting, but in the end he should overcome it like Itachi did.