Just to shed some light on residency matching and so forth. As someone who knows how the process went down this year, I will tell you that almost all the students from this year's graduating class at Mayo had their pick of programs. Almost everyone matched to their first choice (40/42). For many their first choice was Mayo Clinic, way before MGH, Brigham, Hopkins, etc. On that note, I can say from experience that several who stayed at Mayo got the "I'm calling/writing to let you know you were ranked to match...are in the top 3 ranked applicants...,best applicant we've had to our program this year.. etc" from MGH, BWH, JHH, UCSF etc (myself being one of them).
Secondly, going to Mayo Medical school certainly does NOT lock anybody into any program at Mayo. Several of the programs at Mayo, especially those that are very highly desired and ultra-competitive on a national/international level (i.e. ortho, neurosurg, ent, radiology, derm) are extremely competitive whether or not you go to medical school there. So for the student who said "At very worse, you can rely on matching back to mayo," you better publish, ace your rotations and smack the **** outta Step 1 if you wanna match into something competitive at Mayo (sorry to be the bearer of the truth).
Thirdly, as far as program directors not knowing "old friends from Mayo." If you've been to national meetings you will soon realize, the top-dogs on the American Board/College of (insert any specialty here), either are on staff at Mayo or trained at Mayo at some point in their careers (ESPECIALLY in the surgical arena). The staff at Mayo are some of the absolute leaders in their respective fields. Chances are, if you're not at Mayo, MGH, Hopkins, or UCSF -- the guy writing your letter of rec from your school (even at Yale) probably wishes he was boyz with the department heads at the Mayo Clinic.
That said, I'm sure Yale is a great institution and I think you can't go wrong with either choice. But to say that you would somehow be disadvantaged at Mayo is just ludicrous. Bottom line -- if you've got the scores, the grades, the research, and the effort, with names like Mayo or Yale following you -- you're gonna be kicking ass and taking names on the match trail no matter what. But I will say, having rotated at, and having gone to some of the highly touted places on here during the residency interview circuit, Mayo Clinic, to me, is one of the best training programs in the country - period. As for med school, go where you'll be happy. If that's New Haven, CT go, if it's Rochester, MN go. Truth be told, both towns aren't anything to call home about if you're into fine dining or the best hip-hop clubs (but Rochester is certainly one of the nicest and most convenient places to live if you don't mind travelling out for your dance club fix). If you want the proximity to NYC, heck, why live in New Haven??? Go to Columbia or Cornell.