I am not sure if they're pin compatible, but you can check InveSense, there are pictures of packages with what functions particular pins have.
If they're compatible then 6500 is supported inside MPU9250 driver in firmware, so should work (except 6500 does not have Mag). Besides that MPU6000 has smaller (better) noise levels than 6500/9250, so I don't know why would you want swapping, but sure you could do that if they were pin compatible (check datasheet).