The more I think about this whole shameful farce the more I believe the real target was Belichick and they wanted to kick him out of the league, lifetime ban. Or at least a year.
I think it's pretty simple, the Patriots are basically a lock to make the Divisional round. They can't stand Brady and Belichick getting there easily every year. Even when things don't go easy, like in 2013, BB still did an OUTSTANDING coaching and GM job, building and fixing a roster on the fly. No one would make to the AFCCG without 8 starters or so.
BB owning the Ravens last January, coming back from a 14 point deficit twice, using that scheme with the ineligible receivers was the last straw. BB owning every trade he does making every other GM looking like a fool might have played a part on this too. A bunch of owners might have simply demanded that to Roger "LISTEN YOU USELESS SOB, WE CAN'T STAND THIS GUY ANYMORE, WE NEED HIM OUT OF THE LEAGUE, IT'S HIM OR YOU".
They couldn't plant the seed the way they wanted to incriminate Belichick in the process. It was the desperate attempt, they were sitting in that information about the balls from a long time I believe (it gets Cold in Boston way earlier than January) waiting for the right moment to use that ammo, they didn't have the perfect situation but it was good enough and their only shot because the SB was going to be in the desert and in a dome. They got Brady in the process and even though the SMELLS REPORT cleared BB and the Pats organization they still stole 2 high draft picks to make BB sick to his stomach to the point of retiring or going vocal falling into a trap.
The draft picks makes no sense if the investigation is on the QB as it is now. Yet, even the most honest owner when thinking about this whole issue might have thought "Well the Patriots losing picks and their QB for 4 games doesn't hurt my franchise at all", this could be the rationale for 31 owners, even those who don't play in the AFC or don't play the Pats this year. That's why they put Kraft in the wall and said "Bob, YOU WILL HAVE to accept this penalty".
It's all part of a plan to take the Patriots out of contention for the remaining years of the Brady window. They connected all the dots, the Pats without Brady will have a hard time to make the playoffs, he will get back to the game rusty, if the Bills and Jets live up to their investments it's not hard to imagine the Patriots getting knocked out of the playoffs with 6 losses. In this case they will get a higher draft pick than they are used to, let's get this pick too and avoid any trade. They even covered the Garopollo shining trade bait scenario. The trade off is that if he is the real deal they will have to face the Patriots having a good QB for another 15 years.
Next year Brady will be 39 and without a first round pick. The next 40 and without a 4th that is BB sweet spot in the draft. They basically are trying to end the dynasty years and avoiding a new one on these remaining years.