I guess it comes down to you being hung up on spygate. I've read your article, now you read mine and let me know what you think:
http://yourteamcheats.com/what-is-spygate
[I understand it's not the most professional site, it does gives some good insight, though, especially to those who are completely anti- Brady/Patriots].
Number 1, as I've mentioned, this isn't something that went on for the majority of his career, and number 2, it wasn't as influential as you seem to think, and your Madden comparison is not a very good one. And really, just look at the results since. The Pats have continued to dominate, even more-so offensively.
As for those other QB's, you'll have to explain 'inferior stats.'
Manning has a case for being better, but it's a dying one. You've pointed to a 3-2 playoff record for Manning against Brady as if this is the be-all-end-all. The fact that Manning only ended up with 2 rings, versus 5 for Brady, and that Brady has the far superior playoff and Super Bowl numbers kill Manning in this debate. The one thing Manning always had was the regular season success, but Brady has closed the gap in that regard with 2 MVPs, and a chance at finishing with close to as many TDs and passing yards with way fewer INTs while already passing him in regular season wins [plus a dominant record against Manning during the season].
With Rodgers, he might be the most dominant QB I've ever seen; his issue is that he's done it for half the length of time as Brady, so it's tough to bet on him getting anywhere close to 5 rings and all the dominant playoff performances, or 200+ wins, plus all the other career numbers that Brady has. It's possible, but as of now, it's too early to put Rodgers up there.
Brees is a level below for sure. He's been the QB of the most pass-happy team in the most pass-happy era. The guy has made the playoffs less times than Brady has made it to the Super Bowl. He has no MVPs even with all the regular season success. Him and Brady are neck and neck in TDs and are close in yards, but Brees has 70 more INTs and the W-L record isn't even close.
It boggles my mind that you can't admit to him being an all-time great.