I'm thinking that he is not over his injury issues, or is at least managing them, and we've got a 70-80% player for as long as it takes. This happens a lot in football, and it's not helped by the lack of rotation and modern fixture list. Physically he doesn't look right to me.
There are tactical and maybe confidence issues (I'm not so convinced on the latter, as he doesn't seem like that sort of player) as well but I think this goes a bit beyond a player struggling in his first season. The way Atalanta play suited the way he facilitated moves, especially in transition with how they create space and are dynamic. You can see his vision but it's really not working with the rest of the team. I think he's talented enough that he should come good eventually, but there's question marks on whether that's under Motta or someone else, and whether he will ever reach Atalanta levels simply because he's out of that perfect environment and being tasked to do different things.