I don't think Manning and Harbaugh would have come to an agreement on how to run the offense in SF. Considering that they narrowly missed going to the superbowl last season, there's not a whole lot to fix. That division is still rather weak (though Seattle looks to be improving) and there's little doubt that the Niners can win 11+ games and win the division at least. I think Harbaugh likes to run a conservative offense and pound the ball with Gore. That defense is stellar and will always keep the niners in the game.
There may be more 'upside' offensively in Denver. We know they can run the ball very effectively and there's a young and very athletic set of receivers in Denver as well. I think Fox will let the offense flow through Manning and although Fox was clearly a run-first coach while in Carolina, he does know how to remain flexible and change things around to suit the talent he has.
Manning is also perhaps the best student of the game. His preparation is second to none. He also has extensive experience playing in the AFC and would likely be hitting the 'reset' button should he change conferences.
One might also look at the AFC west...you have a San Diego team that had their chances and while they still have some terrific players, they don't have their top wide receiver any longer and one has to wonder how long Gates can remain effective (he turns 32 in June). Oakland has some wonderfully talented players on offense, but this team hasn't been in contention for over a decade. That leaves KC and I'll give them the benefit of the doubt. They were really banged up last season.
Regarding Tebow: don't be surprised if he winds up in Florida. Miami or Jacksonville could pick him up. He's still very popular in Northern Florida.
Cleveland? Eh, they got a decent QB and McCoy has just a season and half of experience. I think they'll give him at least another year.
Maybe the biggest concern is the pass blocking in Denver...