As an intern at the Brigham/Mass General program I can answer some questions about the program. We spend about half our time at each institution (in addition to Children's and Mt Auburn), and there are some significant differences between the two institutions. The Brigham is our administrative "home", but we have offices, lockers, faculty, etc at both institutions (conferences rotate weekly between the two).
At MGH, I think it is true that since surgery ran the ED for almost 200 years up until about 10 years ago, there is some tension there, but to put things in context Harvard is one of the last big academic institutions to embrace EM and one has to recognize that fundamental changes take time (interestingly, this is not really an issue at the Brigham). However, MGH is an amazing place to train - basically the top residents from every specialty under one roof along with great nursing.
The strengths of the program that appealed to me were happy, fun and smart residents/faculty, the opportunity to train at some of the best hospitals in the country (and benefit from very strong residents/teaching in off-service rotations), living in Boston (don't underestimate the impact of which city you will be living in, especially if you are with a significant other), a veteran and receptive residency director, a nationally recognized yet accessible chairman, and a track record of program graduates going pretty much wherever they want as an attending.
If you thrive on penetrating trauma (we get enough to be competent by the time we finish but in general Boston does not see very much), require a place where EM has been entrenched since the early 80's and has completely sorted out all issues with other services, must find an apartment to rent for well under $1000 a month or absolutely can't stand the idea of training for 4 years it's probably not for you.
As you can probably tell I am very happy here and would be glad to answer any other questions you all may have. Good luck in finding the right place for you.