The fact (and it is indeed a fact) that Goodell lied about Brady's explanation for his phone calls to Jastremski should definitely factor into the case. Goodell used that in his decision to uphold the appeal, but it was a lie. That is an unfair/incorrect use of his power.
Another big factor is that Wells testified as saying he did not want Brady's phone and that whether or not Brady handed over his phone/documents would not factor into his decision. That further suggests punishment was handed down unfairly.
Finally, the fact that Reisner was doing the questioning at the appeal hearing yet was also part of the investigation undermines the independence of the investigation altogether.
There's a lot that reveals this whole thing to be a complete sham, but I think those three points should be factors in the actual case. (I'm not a lawyer, but I have a good feeling about this Judge Berman).
Alternatively, the NFL will realize that they now look like complete bumbling fools, and will "do the right thing", own up to it, and exonerate Brady/reduce the suspension. But let's not kid ourselves.