There's a lot of multiple winners of Super Bowls that won't make the Hall. There's actually a lot that don't belong in the Hall, too (Bradshaw). Being a Manning doesn't mean anything, but I guess that gives him some credibility(?)
His career numbers, especially in an NFL that has far surpassed the high-powered offenses of the 80's and 90's that had legitimately elite QBs, are barely above average. Hell, the actual Super Bowl wins were pretty much decided by one pass each (the catch and the drop).
Then again, I sort of think Brady is a by-product of a great system. His backup took them to 10 wins, after all. But his numbers are pretty hard to argue against, with or without weapons.