The Materials Science option at Caltech has been, in a way, combined with Applied Physics, but they're still offering two different degrees. I think if that continues will depend a lot on who becomes (or stays) our department head.
I think, generally, the name of the department will tell your the flavor of MSE you're going to be seeing. Will you be taking more classes in things like plant design or nucleation & growth theory? Will your program focus on a specific aspect of materials or will you be required to take classes on metals, polymers, ceramics, semiconductors, etc?