Pros
I was with a small research team without patient contact, so my experience may be different from most employees. I was working with, for the most part, a friendly, talented, hard-working, interesting, diverse team. The benefits were good, which partly made up for the low salary. Besides the usual types of benefits, there were a few little perks, discounted Charlie cards, movie-passes, and health clubs, a farmer's market, a few free classes, such as yoga and meditation (although I think neither still exists, however) etc.
Cons
The salary was low, even for research. At the time I left, salaries were frozen and they were continuing to cut back on perks. Some of the people were easier to work with than others, although that can happen anywhere. The management, although not too bad for a large organization, occasionally put up bureaucratic hurdles to doing what needed to be done.