I hear this argument quite frequently on the boards, not just in this specific instance. A younger and inexperienced guy is supposedly no good if he can't overtake an older, more experienced player in front of him. In 2012, Jameis Winston couldn't unseat EJ Manuel as starter. Sure he was only a true freshman, but if the theory that talent is the only thing that matters, then why did this happen? Believe it or not, most guys improve over time.
In addition to this basic fact, the dynamics of the qb position last year were complicated to say the least. Nobody says Vad's problem was lack of raw athletic talent. His problem was he didn't trust or like the system and felt his passing talents (in his mind) were being wasted.
I think CPJ was walking a tight rope. He knew he had two talented qb's, one with limited experience and one with next to none. Vad's issues, I'm sure he felt, would get worked out over time and his full potential would eventually be realized. All of this assumed a full buy-in by Vad which we later learned was far from being the case. JT had issues of his own that needed to get worked out over time, but you only have one ball on game day. What's a coach to do?