A few reasons why the Pats could and probably should win this game:
#1 Manning and the Colts just barely squeezed by the Chargers in a game in Indy a few weeks ago. The Chargers have the NFL's worst pass defense, and nowhere near as fierce of a pass rush as the Pats are capable of.
#2 Manning has struggled when playing against teams that employ a 3-4 defense. Check the numbers. People were predicting 60 TDs for him until he met up with the Texans/Ravens/Chargers in consecutive weeks and only threw 5 TD passes. Most people are expecting him to throw 5 TDs this week given the Pats secondary problems, but that's just not likely to happen.
#3 The Pats will be able to move the ball on the Colts defense, especially via the run and Corey Dillon. As long as the Colts defense has to respect the run, Freeney won't be able to tee off all game on Brady like he has to other QBs lately.
#4 Bill Belicheck has had an extra week to devise a game plan, and he has plenty of talent in the front 7 to disrupt the Colts offense (with or w/o a 100% Seymour). I also have more faith that the Pats defense will be able to get a key stop late in the game than I do about the Colts defense, and I give Brady the edge over Manning in a close game.
Should be a great game, but I just wish there was a way for both teams to lose.