Brady's agent Don Yee just came out swingin' ... saying the entire investigation was not only flawed, but carried out by people who have a "limited understanding of professional football."
In a statement, Yee says ... "The Wells report, with all due respect, is a significant and terrible disappointment. It’s omission of key facts and lines of inquiry suggest the investigators reached a conclusion first, and then determined so-called facts later."
Yee even suggests that the NFL cooperated with the Indianapolis Colts to run a "sting operation" with the end goal of embarrassing Tom and the Patriots.
Yee also suggests that Ted Wells was not truly running an "independent investigation" -- because his firm makes a lot of money off the NFL ... and is heavily influenced by the league.
There's more ... Yee says Tom was NOT difficult with investigators and "made himself available for nearly an entire day and patiently answered every question."
Yee continues, "The Wells report omitted nearly all of Tom’s testimony, most of which was critical because it would have provided this report with the context that it lacks."
For the record, Yee never flatly denies Brady's involvement or general awareness of Deflategate ... but says there's definitely more to the story.