There will always be comparisons between these two, and it's something analysts and fans will relish (or get absolutely sick of). That being said, what one is doing ought to have absolutely no bearing on what the other is doing, if the head coach has any conviction at all (and if he doesn't, then why is he the head coach?). You have to go with what's right for the player, not what will save face for you or the organization (or the player, for that matter).
As far as Wentz being pro-ready, it was brought up in numerous places that the system-adjustment would be less of a burden to him. It was one of the main selling points: he played and succeeded in a pro-style system. What pushes Wentz back is the lack of game experience, the lower talent levels he played against, and important traits like accuracy, footwork, and poise. He didn't look any better than Goff in his brief action, and actually, from a throwing perspective, looked markedly worse. Was he more comfortable in the system? As expected, he was. Will that matter in two months, or two years? Not at all.