The reasons Brady is over rated all have to do with reality and facts.
Considering the site we're on here, dealing with sports questions in the hypothetical should not surprise you.
YOU SAY leading in a stat category is evidence of being a great quarterback.
I like to look deeper, beyond just the stat, to find what it really means - and in Brady's case, it means he played in a system that certainly aided in those stats. It also helped a great deal when the Patriots went out and found players who fit well within that system and have a lot of talent on top of it (hence why the talent on the team increased over time).
Look at the evidence: Brady produced good stats within the system. When the team got players who fit the system better, everyone improved stat-wise. When incredibly talented players like Moss were introduced, suddenly the team was phenomenal. It was the changes to the system and to OTHER PLAYERS in that system which generated better stats, NOT Brady.
Cassel's year with the Patriots should kill all doubts the system had nothing to do with it and that it's all Brady. Unlike Brady, who has always been with the Pats and the system, we can compare Cassel in the system with Cassel outside the system (and the team).
Funny, Cassel with the system and the team is much better than Cassel without those things. It's not a huge leap to extrapolate that same phenomenon to Brady and say he would not be nearly as good without the system and the team as well.