If you have tom brady, you don't run read-option's and bootlegs. You're more comfortable with quick passes because he can diagnose the defense pre and post snap better than anyone.
If you have TT, maybe you don't run anticipation timing routes. Why play to your player's worst attributes? Why not use read-option to get the defense moving horizontally, and adding some guess work. Why not pass from shotgun more? He has a better depth to avoid those batted balls, and he seems better at escaping pressure when he's in shotgun. You can also do Run-pass options out of shotgun.