I would prefer to see the Pats beat the Colts at full strength with Peyton for the same reason that beating a video game on hard is much more satisfying than beating it on easy. Rising to a great challenge is what makes great players, great moments, and great memories. If the challenge is not up to par, the achievement becomes forgettable.
Boxing historians often lament how Tyson never had a great rival to really make his career stand out, to truly test himself and be the best (like Ali/Frazier).
For these same reasons, during the almost perfect season, I was decidedly in the camp where I wanted the Pats to try and be perfect rather than take the approach of resting the starters for the last couple games. Even though that didn't work out (and you could make the argument that allowing the perfect season thing to drop by the wayside and resting up players could have made enough of a difference), I still wouldn't have them do it any differently if given another chance. Winning a SB is the goal, but it's not the grandest achievement possible. Quick, without Googling it, who won the SB in 1983? Ok, how about '72?
The super bowl game is merely a construct which makes the game and the league logistically have a goal and structure, but it's the moments of sweat and glory that are the true rewards of the fan.