I badly want the Colts to win (not because I'm a Colts fan necessarily, but because the Patriots are the enemy of all that is good and decent). But I do think the Pats will win.
At least it's not in Foxborough. If it was, you know the Colts would experience one of those famous "communications malfunctions" on a key play.
The Colts are a better team than the Cowboys in most respects, but tey did have one edge the Colts will not: They play a 3-4 defense, which I think is better suited to disrupting great quarterbacks without necessarily breaking down the protection. You're simply not going to beat the Pats' O-line with blitzes, because they'll hold up long enough for Brady to find one of his receivers.
Fortunately for Indy, they don't blitz to begin with, so no worries there - they can play the game they want to. A standard four-man rush with seven in coverage is better, but it helps if you can disguise the vanilla defense, which is easier to do in a 3-4 than a 4-3 (where the QB can assume on nearly every play that the DL is rushing).
I think the Patriots defense is a bit over-rated due to their incredible offense - teams are playing two, three TDs behind early in games, and consequently getting desperate, throwing too much, and gambling to get back into the game. The Pats D doesn't have to be great, just sit back and wait for the mistake to come.
The Colts should move on them pretty well - it's the other side of the ball I'm worried abut.