This is looking worse and worse for the NFL and Goodell, and it's even begun to undermine the wins they had from the last lock out. If I were Goodell I'd call Brady's attorney and offer a one game suspension for failure to comply with an investigation, as Brady has acknowledged he'll agree to.
On a more abstract note, it's funny how the naysayers and "Brady's a cheater" crowd have all but disappeared. The entire Pats/Belichick/Brady cheats concept is easy to understand, just like anti-vax culture is easy to understand. The premise is that "common sense" is sufficient to evaluate and judge a person or event and that scientific inquiry is for "scientists". Businesses (especially sports teams) have existed on the notion that "we have our way of doing it". That's like a pilot saying to passengers: "I have my own way of flying and so we won't be following FAA recommendations on today's flight". (as a corollary this is in line with what the Moneyball book uncovered).
The Pats organization seems to have figured out what few other teams have: that understanding human behavior, taking a strict scientific approach to the game, and knowing the rules better than your opponent will give you the edge needed to win.
I was able to attend a Pats preseason game about 10 years ago (I'm not a fan, but my girlfriend at the time was). We were given tickets from a family friend who had season tickets. We were told explicitly: "Do not cause trouble at the stadium or any where on the property, including the parking lot. The Pats have a zero tolerance policy for disruptive behavior. If they catch you breaking the rules, your season tickets are taken away on the spot. Period."
That exemplifies the Pats organization. Top to bottom they don't f*** around. Belichick has minimal loyalty to keeping players (Welker, Wilfork, etc) because winning comes first. The Pats perennially take players thought to be flawed and maximize their potential because Belichick understands what motivates people. Their system is tuned to near perfection and the expectations are inherent in the culture.
I guess you could accuse me of being a Pats admirer or even a kiss ass. Your g*ddamn right. I admire the Pats the way I admire Google and other businesses who have zeroed in on the science of maximizing human potential.