From what I understand, Watson is more supposed to do machine learning and question answering in order to do something like make medical diagnoses based on the literature.

MetaMed tries to evaluate the evidence itself, in order to come up with models for treatment for a patient that are based on good data and an understanding of their personal health.

They both involve reviewing literature, but MetaMed is actually trying to ignore and discard parts of the literature that aren't statistically/logically valid.