One thing that I have wondered about but really do not know the answer: I have heard that medical schools expect students to have completed their undergrad in four years. If you are currently a junior and if you transfer, you might delay your graduation due to issues with transferring credits or with schools requiring that you complete two full years there to graduate. I do not know what impact this will have with your chances of acceptance to medical schools. It is possible that this might not be a problem.
It seems to me that if you have managed to pull of a 3.9 in two years at Berkeley, you might want to just stick with it, and see if you can pull off another 3.9 for your last two years there.
A GPA of 3.9 at UC Berkeley is very good.