I think there's two stories here with the possible punishment.
With Brady, I was initially thinking a large fine....but it's clear now that the league wanted to listen to public opinion first before laying down a sentence. And if he doesn't get AT LEAST a 1 game suspension, there will be an absolute mutiny amongst the rest of the league and NFL fan bases. Personally, I'm mentally preparing for at least 1 game gone for Brady, and with the team having a week 4 bye this season, it wouldn't surprise me one bit if he's gone for the first 3 games and then comes back after the bye.
Now as for the organization, I also expect a punishment of a big fine, maybe even a draft pick because of their unwillingness to fully cooperate with the investigation. Not allowing another interview with McNally I think is huge, Brady not willing to give his phone I think is huge.
The more days go by, the more I get depressed about this. It's really an unfortunate situation and much like spygate, it was something that didn't have to be done. Regardless now of what Brady does for the rest of his career...I hate to say it, but outside of New England, it's over for him. Regardless of what happens now, public opinion has decided: he's a cheater, his integrity is damaged, and fans and the majority of former players think much less of him now.