I know I'll get flamed for this, but I'm trying to look at the facts, and they conclude what I suspected from the moment the report was broken about balls being underinflated.
I am guessing the Patriots/Brady found a way to underinflate the balls, not a big deal and probably something that has happened many times, but nevertheless against the rules. And as I suspected from the beginning, the NFL would not be able to find the smoking gun that proves the Patriots were involved. And, yes, there is a chance that they really weren't involved, however slim, in my opinion, which I don't present to be 100% accurate but just based on the information given and my own thoughts based on most likely scenarios. In other words, I think it is more likely that the Patriots were able to alter the balls than it is likely that the officials did not properly check the balls (considering the concern had previously been brought up), or that the weather had such a great effect, or that the Patriots were framed. More likely it was the Patriots, but not with 100% certainty.
The question becomes whether or not the NFL will punish the Patriots regardless of not having evidence and also using a "likelihood" analysis. It's unclear what burden of proof they will be using. I can almost guarantee you that later today, Tom Brady will tell the media that he likes the ball a certain way and submits that ball to the officials; if they choose to inflate the ball, deflate the ball, or fill it with maple syrup, he is, and always has, complied with the rules of the league, and frankly, it's impossible for him to alter the balls (he may even go through his pre-game protocol). So at that point, it comes down to reasonable doubt: was the deflation a result of faulty checking/weather/framing/bad protocols or something done afterwards. It is a dangerous precedent to decide this case based on "I believe the officials and I believe the balls could not deflate naturally, and I don't believe someone on the Patriots, although I don't know exactly who or how they did it." Although some may argue the integrity of the game comes first, I believe the integrity of common law is a higher standard and should be upheld by the NFL.
So, in conclusion, I suspect someone on the Patriots did in fact alter the ball but it cannot be proven, and yes, there is always reasonable doubt in anyone's mind. Certainly, it could have been deflated by some other way which we do not know. The court of public opinion will almost certainly favor the theory that the Patriots were involved, and I'm not sure I can really blame them, for better or worse. Luckily, I am used to having my favorite team be doubted and called cheaters, so it is really nothing new.