Having now read the report I would say:
Patriots Organization - For allowing employees to break the rule, or not properly supervising employees so that rules were broken (culture anyone?): Max Fine - I think that may only be $500,000. Loss of multiple draft picks next year including a 1st round pick. [Spy Gate penalty was $250K and loss of either a 1st (if Pats made the playoff) or 2nd and 3rd if Pats missed the playoffs.]
Additionally: For not fully cooperating with the investigation by not having the the guy who did the deflation at the AFC Championship game appear for a requested 2nd interview after the forensic work was done on the telephones and the text messages were recovered. Another Max Fine and an additional loss of a 1st round pick the following year.
I would also have them pay the cost of the Wells Report - probably another $250K or more.
Brady - Max Fine ($500,000 if that is it) Suspension for 4 games for knowingly participating in efforts to break the rule, and an additional 4 games for not cooperating fully with the investigation process by turning over his telephone as requested. Losing 8 games pay is not going to send the Bradys to the poor house, but it does effectively increase the "fine" to several million dollars.
I do not see how the NFL can really do much less in light of the Spy Gate penalties and the statements made at the time, and the relative weight of this issue vis a vis say a player getting a 4 game suspension for failing a recreational drug test.
Additionally, the Patriots messed with league folks and intentionally set out to break the rules - again. Per the Report, the week before the game the Colts notified NFL Rules and Security folks that they suspected the Patriots of using underinflated balls and that they wanted special precautions taken to ensure that the balls used in the game complied with the requirements. The Report refers to a heated discussion in the Press Box between the Colts GM and NFL personnel when, during the 1st half of the game the Colts took possession of an under-inflated ball following an interception and informed the refs, Colts team officials and NFL Security. I think we can pretty well guess what was said.
The game officials also were put into a bad position (that may come back to haunt the Patriots too). The Report describes how the head official was basically frantically searching for the game balls minutes before the start of the game, and of course, they look like idiots for not suspecting something fishy going on -- but realistically do you think they could tell a nationwide audience waiting for a kick off - "wait we just need a few minutes here to do some testing of air pressure on these balls"
Finally, it is clear from the report that this was not a one time thing. It obviously went on for multiple games this past season and even before (in a text message in the prior off-season the guy refers to himself as the deflator).
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Having said all the above, == The rule itself seems ill advised to me. Given all the other stuff they let the teams do to "prepare" game balls it seems like they should either: (a) let the teams prepare the balls anyway they like with the exclusion of putting any sticky substance on it or changing the shape/dimensions; or (b) Have the NFL provide the game balls prepared in some consistent way - sort of like how umpires prepare baseballs for games. Players and teams could have input on how the league should prepare the balls, but other than that -- play with the game balls brought by the refs.
As an aside: The description in the report of all the effort teams go into to prepare the game balls is pretty interesting. The literally spend several hours prepping each ball. The Report is very clear that Brady was very interested in the inflation level of game balls.