The whole system QB debate is so dead and buried. I think we have enough history behind us now to realize that no matter what system you place a guy in, HE is going to have to play well in order for it to work. For example, look at how many QB's have run the West Coast offense? But how many of them have been successful? Not many, and the guys that were most successful are sitting in the HOF right now (Montana, Young, Elway). Steve Bono played pretty much his whole career in that offense and I don't think he will be getting any HOF votes, but that's just my wild guess...
Bottom line and fact, the QB makes the system successful not the other way around. Any Coach at any level will tell you that. And Brady has proved unarguably that he can be successful in a controlled passing system or a wide-open system.
Also, in terms of what happens on breakdowns, I'd say historically that's been a Manning issue. I could point to lots of games where once pressure came on a regular basis Manning crumbled, and I can point to games where the same happened to Brady and he didn't crumble, Super Bowl 42 is a perfect example as he'd gotten smashed up all game long yet never threw a pick, had solid numbers, and still was able to get one last 4th quarter comeback drive in... unfortunately for him, Eli put together his own right after.