His physical ability is unquestioned and impressive. But there were some devastating pre-draft assessments about his lack of maturity and inability to deal with adversity, some of which played out this year when he started pointing fingers for their struggles.
And even bigger picture, it looks like Kap has the kind of gym rat/bookworm mentality that really helps at QB. I can't say Newton isn't a hard worker, but his success came with a highly simplified offense where he didn't have to make reads.....whereas we see Kap making incredible reads, showing that he does his homework AND understands it. Even in his 2nd year at the helm Newton wasn't showing anything like that kind of command. No doubt Harbaugh and co. probably hugely help in this dept.