I would imagine it had to do with a few things.
-a one-dimensional offense that didn't pass much until they had to late in games, meaning defenses could blitz and tee off
With Mike Pouncey and Jake Long, they've got two really great cornerstones, both Pro Bowl-quality players.
Denver's left tackle Ryan Clady is a 2-time Pro Bowler.
Speaking of one-dimensional offenses, Denver threw the ball less than any team in football.
Poor QB's: I assume that most of you think that would apply to Denver.
I don't disagree that all of those things are legitimate gripes, but they're even more legitimate gripes for Denver. Personally, I think that Manning will choose Miami, but I think it has more to do with playing in a warm climate than anything else.