MLB.com has tweaked its Gameday application a bit. If you go to the Boston-Texas game, you will see a button in the upper right that says "Options". You can turn off the pitch trajectories, although you will still get the readings on speed and the mysterious pFX figure in the upper right. You can also change from 3D to 2D animation and you get an easier to follow picture in my opinion.
The big ad in the lower right is still there and it can't be resized, but at least the application doesn't seem to be as much of a CPU hog.