Peyton Manning was A historically great player, but should have been THE historically great player of the modern era. Reasonable scoring systems not ranking him #1 overall IS his failure.
With his pedigree, football IQ, durability, general talent, supporting casts and so on he should have been the undisputed GOAT... but he didn't quite do it. He was set up to succeed as an NFL QB at basically every step of his life. He had a Hall of Fame head coach and GM for most of his career, rules were rewritten to accommodate him personally, he got to play in a dome, he was almost always surrounded by great offensive weapons. Peyton Manning wanted for virtually nothing, ever and nobody ever unfairly held him back in life.
There's probably a good argument in there somewhere about how being set up so completely to succeed ultimately set up his (relative) failure, but that's more in the realm of psychology than statistics.
There's a lot of really tough breaks that quarterbacks have gotten thoughout history...which is why it's really hard to fathom Manning's playoff failures. I don't recall a single season - not one - where he didn't have two very good/elite wide receivers as a minimum. I don't recall any times when Harrison, Wayne, Clark, Thomas, Welker, Decker, or really anyone actually missed a postseason game at any point, or where a wide receiver dropped a wide open pass, or any bad break he got.
Sammy Baugh, like Manning, won two championships and it's surprising because he could have won more. But in the 1943 Championship, he came in with an injury and aggravated it early on; he was barely able to throw and the Bears scored 41 points. Two years later, he returned and lost to the Rams on a pretty bizarre, controversial call where he threw the ball out of the endzone, it hit the goapost, and it was ruled a safety (they lost 15-14.) The rule was correct, apparently, but teams weren't even aware of it and they changed it the next year.
Roger Staubach also won two championships, and it seems like he coud have won more, but he, too, had some more difficult things to deal with. He started his career at age 27. The Cowboys made it to SB5 and Landry named Craig Morton the starter, who promptly went 12/26 with 3 picks, and they lost 16-13. The next year Staubach went 10-0 with a league leading passer rating. He was 29 years old when he became a starter. Then in his two Super Bowl losses, he faced the Steel Curtain defense, plus there was that infamous Jackie Smith touchdown drop in SB11.
Steve Young was 31 years old when he finally got a full season as a starter, despite being the top pick in the supplemental draft in 1984. Bad, bad teams (Bucs), crappy leagues (USFL) and an all-time great quarterback (Montana) all led to some extreme circumstances leading to his short career. And when he finally took over, the absolutely stacked, dynasty Cowboys were waiting.
So these are 3 guys very often in the mix with Manning on the all-time rankings, and with them, there's a whole bunch of "what could have been" and it's pretty legitimate. With Manning, it's the opposite; looking at how one can get every imaginable break, including maybe the biggest "freebie" championship in the Super Bowl era.