Pros
It differs greatly by department -- some are excellent and some are not to be recommended. In my department , which is focused on cancer research, there is a great deal of academic freedom. Any area of research I would like to pursue is open to me, as long as I can secure the funding and be productive. I have found the people to be highly collegial, and the environment is very research-oriented, so resources are generally good. The grants office does a good job of assisting with the completion and submission of grants, and the IRB is very easy to work with and relatively quick. The institution, which was struggling financially in the early 2000s, is now strong and appears to be heading in a very positive direction. Thus, the outlook is very good.
Cons
PhDs are not as highly respected as MDs, and there are relatively few awards open to us. That can make it difficult to add important honors and awards to our CVs. The quality of the departments varies (however, that is likely to be the case at many large institutions). Some of the red tape is terrible. Accounts Payable is particularly bad, and getting contractors paid can be a hellish and time-consuming experience.