You make fair points, but I think it's still evidence that the Pats have generally had better teams and more complete rosters than the Colts. I know the Brady vs. Manning debate is one that will rage on forever, but I don't think many will debate the quality of rosters the two teams put out. It's certainly not the only or most substantial evidence, but I think it's contributing evidence to the argument that Brady has had more help than Peyton.
Looking forward to seeing your response. However, I must put forth a rebuttal to some of your points.
Regarding the bolded, I think it provides evidence to support my argument. The Pats had better quality backups. In other words, they had better quality talent on the roster than the Colts. That better quality talent on the roster allowed them to win, even when their HoF QB was out. The "ifs" and "buts" of "if Arizona made that field goal..." aren't really relevant. At the end of the day, the Pats won and went 3-1 without Brady. Whether they were close wins, comeback wins, or blowouts, they won. That's what I'm arguing here: the Pats have had better quality talent on their roster, making things easier for Brady. That doesn't mean Brady hasn't made a huge contribution, but that things have been slightly easier for him than they were for Peyton.
Regarding the underline part, you're ignoring the huge changes involved. The Colts went 11-5 in the three years after Manning left. They also changed nearly the entire roster, entire coaching staff, starting QB, etc. 2012 was nearly a completely different team from 2011, let alone 2013 and 2014.
Lastly, 2011 wasn't just an off year. It wasn't like the injury bug just bit the Colts hard and the ball didn't bounce our way. The entire team was a mess. The offense couldn't sustain a drive, the coaches couldn't gameplan to the (lacking) talent on the field, the defense was always on the field and getting picked apart at will. It's no surprise that there were so many changes from 2011 to 2012.