Harbaugh deserves a ton of credit regarding QB play. He's never had anything but good QB play, and that is largely because he implements an extremely QB friendly system that dumbs down post-snap reads. During the Kaepernick bone-fest last year, I paid closer attention to his game. Hardly ever, did he progress to a second read. Now, this isn't calling Kaepernick stupid (which has nothing to do with reads), but rather an observation that I continued to see.
After I kept seeing this trend, I hit up Doug Baldwin on Twitter to ask if indeed, the Harbaugh system is uber easy on QBs, to which he replied "YES." In summation, he told me there are 2 variations of the play call and the QBs job, pre snap is to verify the look the Safeties give. So, when you hear people scream "look at him audible," he's not really calling an audible. He's simply adjusting the play variation in accordance to the Safety look. This is why the 49ers continually take a ton of time pre-snap, because it's much easier on a QB to do most of his "reading" before he actually has the ball in his hands and the play is live.
Most of all, this makes sense. Harbaugh's continuing trend of QB play, no matter the QB, really is an admission that he truly is an offensive genius. He simply makes QB life extraordinarily easy.
If he is involved in player evaluation (for the draft), then he's pretty average (at best). Kaepernick is good, but I'd argue that any decent QB with talent would be effective in his system. Aldon Smith is a great player when he lines up next to Justin Smith, but was wildly average when he (Justin) was hurt.
Lastly, Harbaugh is just a douche canoe. I find him to be incredibly unlikeable as a human being. No humility whatsoever. I know people think Pete Carroll is cocky, but he's also outwardly a very accomodating/nice guy.