You are right, there are missing pieces but he can still develop them over time. Issue is he has been forced into the halfback role in a system that is heavily reliant on halfback dominating (look at Penrith with May instead of Cleary) when he has spent more time playing fullback, centre or 5/8. If you actually watched some of him in the lower grades then you would see his style of play has totally changed.
Baz has to move him to a different role or rest him to try and protect him and get him back to doing what he's actually good at instead of trying to manufacture him into the halfback he wants. Then again Baz compared Flanagan to Cleary so fuck knows where his head is at.