I think Milton is a classic example of a trap for a coach's ego. He has every measurable that you'd want in a QB. He's got a cannon. He's strong and fast. He's tall. I think coaches see guys like Joe and think "If only I could coach him, I can unlock his potential". Pep Hamilton and Harbaugh couldn't do it, but his next coach's ego is saying "you can be the one who fixes him."
My take on the two games I've seen of Milton is that he doesn't have an innate feel or awareness of the game. He has no touch on the ball, and he doesn't seem to understand the game well enough to sense pressure. He's also telegraphing almost every read as he goes through progressions.
Hooker definitely has his own flaws, but are his flaws actually fixable by further development. I'm not sure any coaching staff could teach Milton to scramble like Hooker. Hooker has a flow to his running where he can be shifty. Milton is hesitant and stiff as a runner.
We'll see how Heupel moves forward with this QB shuffle. Hopefully, he won't get caught up in his ego and force Milton, if Milton can't show a better feel for the game in the next few games.