This thing is far from over.
The NFL Players Association have appealed the league's decision on the behalf of Brady, and requested an independent arbiter.
The Patriots have a highly capable law firm on retainer (Morgan Lewis), and a senior partner for that firm (Daniel Goldberg) sat through all of the Wells Investigation interviews with Patriots personnel.
Goldberg has already published his reply to the Wells report (
The Wells Report in Context), and, basically, torn it to shreds.
They have fully credible scientists (unlike the buffoons hired by Wells) who have detailed scientific explanations as to how the balls measured what they did at halftime without any tampering with the air pressure.
Brady refused to hand over his cell phone under the advice of counsel and the NFLPA. Not because there was condemning evidence, but rather because it represents a bad precedent for other players in similar investigative situations in the future.
"More probable than not" in the Wells Report is a subjective opinion, not a preponderance of evidence.
In the event that the entire situation is not reversed during the appeal process (which it probably would with an independent arbiter) it is quite likely that Brady will sue the league. That is an option for him, and based on available evidence, he would most likely prevail. While the team cannot appeal league penalties, individual players can represent their own interests.
This is most likely going to be Goodell's swan song.