Not quite sure what to make of this case yet. Certain parts certainly seem flimsy while some other stuff does make you raise an eyebrow.
One thing it has illustrated, however, is the ridiculous double standard by the media & general public in regards to how Manning has been treated by the majority (innocent until proven guilty) versus how Brady was treated in the initial aftermath of Deflategate (burn him & the Pats at the stake).
None of this PED stuff is ever surprising to me, I agree that the far more interesting angle is in regards to the media coverage/spin, or lack-thereof. There are a couple of different distinguishing factors between Brady and Manning:
1) Brady is lumped in with the signal scouting and could be viewed as a "repeat offender".
2) Many just assume "All these guys are on something" so PED's do not have the same cheating stigma they once had.
3) Manning has been a lovable goofball through ads, so he is viewed upon more favorably than the super model looking Tom Brady who is picky about his national ad campaigns.
4) Brady has won far more on the New England Patriots.
5) People/media hate Belichick, who has been giving grumpy press conferences for 15 years.
I might be forgetting something, but these would be the biggest factors in what is sure to be uneven and "fairer" coverage.