This is tangentially related and I didn't want to dig up the Case Keenum concussion thread (if there was one), but
Florio has an article about how Goodell admitted in an interview today that the Keenum situation was not handled correctly. However, the league already determined that no one will be fined or disciplined for mishandling this situation.
So, the commissioner acknowledges things were handled incorrectly with Keenum. There is clear video of all the events and I don't believe there is much debate over what should have happened when and that a breakdown in the system took place. The league's response was to remind everyone who should have been following the guidelines that they really should be following them. No other disciplinary measures were taken.
With the Patriots last January, there was no evidence of wrongdoing, no witnesses, no video, and no confessions. The benefits, if there were any, are debatable. The league's response was to issue a crippling punishment over what less than 1% of the air in a football (assuming someone actually removed that air on purpose.)
Ask a casual football fan about Case Keenum and most of them won't know what you're talking about. If you wait a few months, none of them will. Ask them about deflategate and you'll the opposite response. The degree to which these situations are screwed up is unbelievable.