Are you seeing pitches largely in the middle of the plate?
I ask because with how the game (seemingly randomly) places pitches that miss, a lot of times I see bad pitches (i.e. bad locations) that I presume are misexecuted pitches. They could have gone way out of the zone, but ended up down the middle instead. Especially in the low minors...I haven't played RTTS this year yet but if what's in AA rosters in franchise is any indication...I suspect a lot of just horrid pitches.
Other than that, maybe adjust strike frequency lower (maybe 0 in AA, halfway between 0 and where ever you usually have it in AAA, and then where you usually have it when you make the Majors)?

Comment