Pros
Yale offers great exposure to great minds and great resources. My experience derives from a fairly narrow existence in the department of ecology and evolutionary biology. Nonetheless, I have been impressed with the lab facilities, libraries, etc. As in any academic setting, I have freedom to explore and guide the outcome of various different facets of my project. There is also ample opportunity to train and work with students and technicians. And of course, I have a great deal of flexibility in work hours. As far as environment, New Haven is a beautiful place to live in the spring and summer.
Cons
I have few complaints regarding Yale as an employer. As with all institutions, a substantial bureaucracy exists to hamper even the most trivial of tasks. Each lab and department has its own culture, and at least some come across as fairly impenetrable to the outsider. This goes for the city as well. New Haven is a small town trying to be bigger than it really is. More Bridgeport than New York or Boston. Winter is cold and rainy and restaurants are expensive. Although several neighborhoods are quite comfortable, many leave a lot to be desired. Oh, and much of the Yale gym is ancient.