Peyton Manning: the better, more consistent, smarter QB. Eli Manning: nowhere near as consistent or cerebral, but the better "athlete" (stronger arm, better mobility in and out of the pocket). Both guys play to their strengths. The result: Peyton Manning varies from very good to great. Eli Manning varies from brutal to a guy who can take a beating and still somehow gun the ball into triple coverage on short and intermediate routes 10 times AND roll to either side of the field and throw the ball up for grabs (also to a WR who is covered) 3 or 4 times a game and have good things happen more often than not. Not classic, textbook QB play the way that Peyton Manning plays the game but it is effective for Eli Manning far too often to be luck.
There is also the issue of the supporting cast and system. The Colts under Bill and Chris Polian had the philosophy of building a franchise to win as many games as possible during the regular season and then take their chances during the playoffs, when they would likely have a 1st round bye and at times home field advantage throughout the playoffs. The Colts also had the strategy of holding onto a few very well compensated stars (i.e. Manning, Marvin Harrison, Reggie Wayne, Edgerrin James, Dallas Clark, Dwight Freeney) while making do with the other positions. The Giants meanwhile under Ernie Accorsi (who built the 2008 Super Bowl team, though Jerry had an excellent draft in 2008 after Accorsi retired that contributed to it) and Reese (this current team is basically his) have had the opposite philosophy: build a team designed to win in the playoffs even if it meant not performing in the regular season (i.e. going 8-8 in 2006 and 2009, failing to make the playoffs in 2010, and qualifying on the last week of the regular season in 2008 and 2011: the Giants have reached 12 wins only once under Eli Manning). Also, the Giants are far more willing to let key players walk rather than giving them big contract extensions.
Another thing: where the Colts frequently used 1st round draft picks on skill players on offense (i.e. Reggie Wayne, Dallas Clark, Anthony Gonzalez, Joseph Addai, Donald Brown) Hakeem Nicks was the only Giants 1st round pick at WR, RB or TE to play on either the 2008 or 2011 Super Bowl teams. Instead, the Giants used all but 1 of their top picks since taking Eli Manning on defensive players. As a matter of fact, in 2005, 2008, 2010 and 2011 the Giants used their top TWO picks on defenders. And the one year that they used their top pick on an offensive player, the 2nd round pick went on a LB. So while the Colts have been building a great offense to win games, the Giants have been building a great defense to win championships.
Also, consider that while the Colts have had the philosophy of taking advantage of having a franchise QB like Peyton Manning by surrounding him with the best weapons possible so that he can dominate, the Giants have for the most part used the strategy of having their franchise QB elevate the play of WRs and TEs drafted in later rounds (by making plays to them throwing the football that most QBs wouldn't even attempt, let alone complete consistently) and similar talent at RB by setting up the run with the pass. Mario Manningham: 3rd round. Brandon Jacobs: 4th round. Ahmad Bradshaw: 7th round. Victor Cruz: undrafted free agent. Jake Ballard? undrafted. Bear Pascoe? 6th round pick. Travis Beckum? Cheap free agent, as was 4th WR/special teams hero in NFC title game Devin Thomas. Henry Hynoski? Undrafted. There are also no 1st rounders on the offensive line. LT Diehl? 5th rounder. LG Boothe? Undrafted. Bass and Snee were 2nd round picks, McKenzie at RT was a 3rd rounder. Add it all up, and the Giants 2 deep offense has 2 first round picks (Manning and Nicks), 2 second round picks (both interior OLs) and the rest were 3rd round or later.
As Eli Manning has two Super Bowl rings and is still very much in his prime (31 years old) despite being a clearly lesser player than Peyton Manning, it is safe to say that the strategy of allowing your franchise QB to elevate the offensive players around him works better than surrounding your franchise QB with the best possible tools to win games by dominating. The Polian strategy results in a great offense but only an above average defense. The Accorsi/Reese strategy results in an above average offense but a great defense. Also, one should point out that the Accorsi/Reese model resulted in more salary cap flexibility, allowing the Giants to go after big salary free agents like Antrel Rolle ($37 million contract in 2010), Chris Canty ($42 million contract) and Plaxico Burress. Meanwhile, the Colts only signed one such free agent - Corey Simon - and it didn't end well.
As far as coaching: a wash. Tony Dungy caught a lot of grief, but YOU try to win a Super Bowl with a defense Bob Sanders is your best run defender (because your RDT is 270 lbs, your LDT is washed up, and your MLBs are nonfactors) and after him your second best DB is a 32 year old guy from the CFL. Give Dungy the Giants defense (either 2008 or 2011) and see what happens. As far as Caldwell goes: his one year with a healthy team, they were a ton of special teams breakdowns away from beating the Colts. And that is ANOTHER difference between Polian and Accorsi/Reese. The Giants had an EXCELLENT punting, kicking and coverage units that in the playoffs. Special teams set up 10 points for the Giants in the NFC title game, and 9 points against the Patriots in the Super Bowl. Meanwhile, with the exception of Adam Vinatieri, the Colts had none of those.
Bottom line: the Colts have (or had) a better QB. The Giants had the better organization and philosophy. Great organization/philosophy with (very) good QB beats great QB and suspect organization. Which is why Jerry Reese still has his job, and the Polians do not.