It is "more probable than not" that Brady had something to do with it...
Having said that, everything about this has turned into a double-standard witch hunt.
First of all, the ESPN report first breaking the story is inconclusive at best considering that a similar method of measuring the PSI wasn't consistently used:
http://profootballtalk.nbcsports.com/2015/05/10/pressure-gauge-discrepancies-undermine-wells-report/
Of course it isn't sexy to read the above article and report on mishaps that happened when measuring the PSI. But that doesn't prove that he didn't do it, Richard Sherman's urine sample was spilled and that was the only reason he didn't get 4 games for PED use so he still did it. Still, players deserve a fair weighing of punishment based on actual...you know, facts.
Ted Wells is not an independent investigator, and if he is - he's terrible at it. Brady doesn't want to hand over his phone because Wells has used past defendants phone records and brought up things irrelevant to the investigation just to embarrrass and discredit those on the stand. It's a low-life lawyer tactic.
So the Patriots and Brady cheated for sure...oh wait flip to page 228 of the report and you'll get this nugget:
“In sum, the data did not provide a basis for us to determine with absolute certainty whether there was or was not tampering as the analysis of such data ultimately is dependent upon assumptions and information that is not certain.”
So he just discredited his own conclusion saying they have no proof.
As some have said the NFL isn't a legal organization...maybe it should try harder to be. If you get 4 games for PED and 6 for beating your wife or raping someone no one's feeling good about fair punishment for any violation in the league.
Why isn't the league investigating the Packers after Aaron Rodgers admitted that he prefers his footballs overinflated? Why isn't anyone talking about Brad Johnson's "legacy" after he paid $7,500 to have his footballs deflated in Super Bowl XXXVII?
Have the Patriots cheated before? Sure. Did they cheat this time? Probably. But the way this "investigation" is shaping up is just ridiculous.