@nfldraftscout: The NFL has paid Ted Wells over $45million dollars to head-up two botched investigations. Great job if you can get it.
Could be that @nfldraftscout is correct about the $$, but not the botched investigations.
So far as I could tell, the judge didn't rule on whether or not Brady was involved in a conspiracy to deflate balls.
Instead, the judge said the NFL's (Goodell's) process was unfair to Brady. Regardless as to Brady's possible involvement in deflating balls, the NFL's penalties for that kind of behavior were never made clear to players (and so it is unreasonable to impose significant penalties for the behavior). Plus, the NFL didn't allow Brady to question people who had knowledge of the investigation, which also undermines fairness.
Could be that Ted Wells was absolutely correct, but that Goodell's office mishandled the situation.