You can go back and forth on if Kaepernick is any good for days but the point is that Harbaugh didn't walk in having his type of QB at Michigan. I think the orginal point that was trying to be made (seeing this is a PSU board) is that Franklin got "stuck" with Hackenberg while Harbaugh was "handed" his ideal guy.
It's a rather uniformed opinion for anyone who belives that. Hack is quite a bit more talented than any QB Harbaugh inherited and he had to get a grad transfer to even put someone on the field that is adequate...a guy that not only lost his job at Iowa but is not in the true mold of what Harbaugh wants...people who think Harbaugh wants a game manager or a guy who just stands in the pocket have clearly not followed his coaching career.
I'm not going to compare and contrast all aspects of Harbaugh vs Franklin on this board. I'm a Michigan guy and a visitor so I will respect my place here. However, I will say that Harbaugh is a qb guy and if there is one single position he is best at working with it is that. So he can adapt to not having "his guy" at the position better than almost anyone if not everyone. That still doesn't mean it is an ideal situation.
You make a good point about Harbaugh coaching/managing his QBs. That's the biggest difference between his situation and Franklin's; Harbaugh did not have a 5* QB who was expected, even mandated, to be the starter. While most people, looking at the surface of each situation, would say that the 5* guy puts a new coach in the best position to win, that's not necessarily true.
Nobody on this board (at least nobody in their right mind) would say that Hack is not, never was, or never will be a great QB. My opinion is that he can be, likely will be, but only if he is in the perfect system with talent around - and especially in front of - him. Franklin's problem was that Hack did not "fit" in the system he wanted to use, so he was left with two choices: try to get Hack to change most of what he's learned up to this point, or revamp his system for the sake of one player. Personally, I think Hack could benefit from learning new ways of doing things, but that's neither here nor there.
Harbaugh's problem is that he felt he had NO QB with whom to work. To his credit, he got someone who fit enough, someone who could be enough of 'the guy' for a year while he hopefully (hopefully for him, not me!) got the next guy in line ready to go. In the meantime, he got a coach who could get the o-line right so that if he has to suck it up and go with a young QB next year, at least the kid won't be sky gazing for most of every game.
Hard for me to say who had it worse, but I think I'd rather have Harbaugh's problem.