Let's go position by position:
On offense-
QB -
Advantage Colts, Manning has proven it. He's had longer to work with good receivers, but you can't quantify how well Brady would've done with better receivers over the last 5 years. Plus Manning doesn't need the Rookie Wristband to know which play to run.
RB -
Advantage Colts, barely. Joseph Addai is better than any one RB on the Pats* roster, but the Pats* in total have a better RB core in Maroney, Morris, and Faulk. Colts have Addai, then the unproven Kenton Keith, then Luke "Nobody" Lawton.
WR -
Advantage Colts, the sum of Harrison, Wayne, Clark (he often plays as a WR despite his TE status), and Gonzales is stronger than Moss, Welker, and Stallworth. However, Moss is the most talented WR of all time when he wants to be.
TE -
Push. Dallas Clark is more of an offensive weapon, but Ben Watson is probably better at blocking and is pretty good receiving the ball too. Utecht and Fletcher are more offensively dangerous than Kyle Brady. Does David Thomas even get playing time?
OL -
Push. Both are playing at a high level right now. If Tarik Glenn were still playing I'd probably say advantage Colts, but both have only allowed 3 sacks this season, and both are doing a good job opening running lanes.
On defense-
DT -
Advantage Pats*, Wilfork is a beast, Colts DTs are both under 300 lbs, one is a converted DE, the other is an undrafted rookie free agent. Granted, they're both playing much better than expected, but Wilfork could eat them.
DE -
Push 'til Seymour gets back. Freeney is very talented and is always creating disruption in the backfield despite the low sack count. Mathis is also a good pass rusher but is inexplicably not getting as much playing time this season. Ty Warren is or should be a Pro Bowler, and Jarvis Green has 3 sacks this year.
LB -
Advantage Pats*. Thomas, Vrabel, Bruschi, and Colvin are possibly the best LB core in football. And Vrabel can catch passes, too! Freddy Keiaho looks like he might be a good player, but Morris just got hurt, and Brackett is good, but there's really no comparison here.
CB -
Push. Marlin Jackson is playing at a high level right now, but Kelvin Hayden isn't on the same level with Assante Samuel or even Ellis Hobbs.
Safety -
Advantage Colts. Bob Sanders is pound for pound the best defensive player in football. When he isn't injured. So this could change quickly, especially if Rodney Harrison comes back strong. Which he obviously will, cos he's been taking his "vitamins"

.
To me they're two evenly-matched teams. The Colts have had tougher competition but have still trashed two of their four opponents. The Patriots* have played garbage teams and have treated them as such.
Once again, it's the Colts and Pats* at the top of the AFC. This time they'll be battling to see who gets to beat the Cowboys in the Super Bowl.