Admittedly, I have followed the story only casually over the years. Certainly there was a lot of suspicious behavior, but if there was clear evidence there wouldn't be such a controversy.
Beyond that 4 game suspension is totally ridiculous for under inflating balls. Instead of trying to setup a sting operation, the NFL should have just asked for new balls and never let the issue see the field. Instead now the integrity of the game was been questioned and for what? Over ball inflation? Plenty of other QBs have gone on record for ball manipulation. The penalties levied against Brady and the Pats were outrageous.
The fact that it is even still a story is an embarrassment. And probably only due to the NFL wanted to dominate the headlines during the offseason. They probably never expected it to get this out of control though.