Goodell's endgame is all about PR.
He's boo'd at every public appearance and has had his competence openly questioned. If the Wells report came back inconclusive and that his office's incompetence contributed to that finding (not documenting psi before game, not sure which needle gauge was used, not testing all the Colts balls at halftime or even after the game, etc…) it would be another PR nightmare for "Goof"dell. He would be criticized for "fixing" the results for his good buddy Robert Kraft or simply condemned for being the incompetent fraud that he really is.
I don't think its a coincidence that Goofdell just had a puff piece released by NFL Network talking about the impact his mother had on his life. It was an attempt to make him look human and likable. The man's image is very important to him, as it should be. Unfortunately, he's just not very good at sifting through complicated situations….In short, he's bad at his job.
Coming down hard on the Patriots was his only win. The Patriots are an extremely polarizing team. The media leaks fed a national outcry and now Goodell looks like the hero who finally brought those "cheating" Patriots to justice.
Having said all this, I do believe this is more complicated than a simple conspiracy. What we have here is the flaw generated by giving too much weight to assumptions. Its a complicated world full of all kinds of different people with different thought processes. Some rush to judgement and some don't. Wisdom is not a common trait amongst human beings. Its rare. Unfortunately, what was needed in this case (and many others) was a intellectual mind capable of digesting information and applying wisdom to the situation. Instead we got stuck with a guy like Wells, who despite his best effort, is prone to basing his opinions on assumptions and faulty logic.