Ehh, considering how low he is in some stats it's not a stretch to improve them a bit. What I did to get him to 99 was.
Agility: 62 to 68
Speed: 60 to 65
Acceleration 64 to 72
Carrying 61 to 65
Throw Power 96 to 97
Elusiveness 48 to 55
Med Throw Acc 97 to 98
Deep Throw Acc 88 to 93
Throw on Run 85 to 95
Only really big changes are Deep Throw and Throw on the Run, but Brady's deep ball has been the best it's been since 07 and throw on the run may be a stretch but he does it when he needs to. The speed boosts also aren't that big of a deal, it's not like he's Mike Vick now. The Acceleration is a bit of an increase, but considering he's still only 65 overall speed I don't think it matters to much.