where Goodell could have investigated and prosecuted this case without getting overturned.

The judge sided with Brady because:

(a) The league gave no notice to Brady (or other players) about the potential discipline that awaited for ball deflation or other related misconduct;

(b) The league didn't allow Brady's team to examine one of the lead investigators in the Wells report; and

(c) The league didn't give Brady's team sufficient access to certain investigative files.

Had the league been more fair in its process, it seems like they would have won this case, and the lousy deal the NFLPA agreed to would have been upheld. In other words, it seems the judge didn't opine that the league has too much power, just that the league didn't use its massive powers properly.