By the end of Final Fantasy 7 I felt it was pretty clear Cloud had broken the hold Jenova/Sephiroth had over him.
As for AC, I didn’t think there was anything in there that showed good enough reason for him to revert to his old self. No, I don’t think Geostigma would have affected him that way - as he was at the end of the game. That’s why I said the just decided to hit the undo button on him.
And even if you were to say that there was justification for how he was acting, none of it was ever shown, not even in flashbacks. It was just a case of him going from “Hurray I’m strong enough to stand on my own two feet and help my friends!” to “I’m a whiny git blah blah blah”. there was, as far as we are shown, either directly or indirectly, no between ground. And all the character development in AC essentially just gets him back to how he was at the end of the game - able to stand on his own two feet and be unaffected by Sephiroth.
Note, by ‘affect’, I am referring to influence his actions by asserting the influence of the Jenova cells in Cloud, not by messing with his mind in more mundane ways. Though Cloud was strong enough to get over that, too.
Edit: Val, he was saying he was a cold blooded Mercenary killer who was in SOLDIER! Of course they were going to take advantage of that, he’d be the perfect addition to the team. She knew something was odd at the time, she didn’t quite know what was going on though. She didn’t know the depths of his fucked-upness at that stage.