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His goal has always been to coach in the pros. Now if he somehow flops, he can ALWAYS go back to the college game where he obviously proved to be successful. On the other hand, it'd be hard to top we he did this past year at Stanford. If he stays another couple years and doesn't do as well, he kind of loses his luster. He left at the right time.
And the 49ers roster isn't worse than the Dolphins are Broncos. So with that being equal, he gets to stay home with his family in the Bay Area. He won't have to move and I think that was big on his list. Don't know how much money Miami offered, but if it wasn't much more than what the 49ers offered, their roster isn't any better and their front office situation (openly searching for a new coach before you fire the current one) seems just as dysfunctional as the 49ers have been.
Plus he'll coach in a division where the best coach right now is probably Pete Carroll, as opposed to a division where the best coach is that Belichick guy. He doesn't really need to work any kinds of miracles to get the 49ers back into the playoffs in that weak division.
You never know how a college coach will turn out, but a guy with 15 years experience as an NFL QB and 2 years as an NFL QB coach is something most college coaches don't have. Plus over half his staff at Stanford had experience on an NFL coaching staff.