Brady and Brees had legitimate excuses.
Brady's problems had to do with inexperience and injuries with his receivers. In the stretch when Gronk was healthy and Dobson was hitting his stride, he was pretty much flawless. If he had Gronk, Edelman and Dobson were healthy all year, and he didn't have to rely so much on rookies early in the season and put up those numbers, I would agree you have a point.
Brees basically had Jimmy Graham and not much else at receiver. Colston is still decent, but not the receiver he once was. Kenny Still showed some potential at times, but disappeared for stretches of games. And the rest of the WRs were mediocre.
On the other hand, Manning was loaded with weapons that were capable of attacking defenses at all levels of the fied. Demariyus Thomas is capable of being one of the better deep threats in the league, but rarely was used that way. Yes, he lost Welker for a stretch, but he was the fourth option of that offense even before he went down.
As for Rogers, was having an inconsistent year to begin with (some games he was otherworldly and others he just downright sucked) and missed nearly half the season. And his receiving corp wasn't nearly as good as Manning's.
If Brady, Brees, and Rodgers all had the two Thomases, Eric Decker, and Welker as their primary receiver and put up those numbers, the I would say you had a valid point. But name the Packer receiver who would have started on the Broncos last year other than Jordy Nelson. Other than maybe Edelman and Gronk (who only played six games), name the Patriot receiver who would have started on the Broncos last year. Other than Graham, name the Saints' receiver who would have started on the Broncos last year. You can't.
The Broncos had arguably the most talented receiving corp in the NFL last year. The Pats, Saints, and Packers all arguably had below average receiving corps last year when you factor in injuries.
Manning's problems throwing down field appeared to be primarily the fact that his balls were ducks. Brady's, Brees', and Rodgers' seemed to have a lot to do with issues with the receivers whether it was talent or getting on the same page or whatever.