I don't think there was any doubt before the second fight who was the better boxer. Just many peeps thought Wilder's ability to knock out his opponents, he'd won 41 of his previous 43 fights by knockout, would prevail. Forgetting Fury had largely outboxed Wilder for large portions of the first fight because he'd been knocked down twice. That second one in the 12 and how he got up from that is the stuff of Boxing legend.
Fury would be favourite v AJ for sure, if for no other reason Fury has the longer reach and would be able to frustrate AJ more than the other way round. As we have seen with AJ so far he has plan A to go for the early knockout (Ruiz fight 1) but got caught badly in that one or plan B - control the fight with his reach and jab (Parker and Ruiz fight 2). So, unless plan A works, which Fury would be too smart to let AJ get close enough, then plan B isn't going to work.