Pros
As a resident in the Partners system, you are working within a large academic community and are around some of the best and brightest. it also provided me with the opportunity to receive great training in a variety of different hospital settings, as the residencies tend to span across a number of hospitals. Partners also has a great number of resources available to be accessed. I felt that the level of compensation for residents and the benefits were significantly better than in many other cities, though Boston is known as the city with overall high rates of compensation (relatively speaking) for residents in training.
Cons
As a resident, the hours worked are long, and opportunities to have a life out side of medicine is quite difficult. Additionally, the fact that there are many of the "best and brightest" unfortunately often means that you also have some of the most narcissistic individuals and that departments do not always work well together, with many departments thinking that they are better than other departments and not respecting their work. Additionally the lack of off-site access to electronic medical records for charting or completing notes etc. was a pain, especially when trying to document phone calls etc. Most other hospital systems of its caliber had a much easier way to access EMR from off-site. While Partners theoretically had it available, the vast majority of us were never able to actually get it to work.