I don't know if this is possible, but here goes.
Let's take this picture of Ryan Howard as an example for my suggestion.
Imagine this was your picture in the game for Howard. You start a game with the real ML roster pack, but after a few years, Howard is traded, or leaves in free agency. We will say he goes to the Yankees.
He's gone from the picture above to:
(this obviously isn't perfect, I did it in paint, but it gets the idea across).
How cool would it be if the game could do this? On one hand it seems like a complicated thing, but on the other...it can do FaceGen, it could surely do something as simple as this. The complicated thing would be being able to recognise where the new logo should go (and if the generated logo would look right on the real hat, I cut the Yankees logo from a picture of Jeter).
I appreciate that this probably won't be used, but it would be a really cool feature.