As much as I would love to attend Mayo, it certainly isn't for everybody and for good reasons, many of which
LizzyM pointed out.
Small class size isn't for everyone. Rochester is a terrible city for young people, especially those from the coasts/bigger cities. Temperature is whatever; students shouldn't make it a determining factor, imo.
From the far more important clinical training perspective, Mayo clinic does not serve a diverse patient population per se. It's a referral hospital and
generally deals with (white), affluent folk. Others can speak to this, but I can't imagine you'd want to do your clerkships at Mayo if you wanted to match at an EM program in NYC. I don't think you would be as well prepared. Of course, also not great if you're interested in urban medicine. I think it's very easy to get caught up in the fact that Mayo is ranked #1 in so many specialties, but it truly depends on the career goals of the individual student. If you have no clue what you want to do, then Mayo will be just fine, but if you're looking for something in particular, Mayo
may not provide that.
No university affiliation generally means less research going on. You're not going to find the wide buffet of research opportunities that a medical school with an affiliated undergrad will provide. My interviewer said this himself. The small class size certainly helps with getting your "top choice" research project from those that are available to you.
Lastly, yes, 90%+ of Mayo students match to one of their top 3 choices. I don't know how well other programs place students into their top choices, so I can't really make a meaningful comment. However, many students that attend Mayo are from the area and prefer to match within the region which may mislead students who go to MMS thinking they can match anywhere they want. Certainly, purely from anecdotal evidence on SDN, Mayo has no problems placing students into competitive specialties and residencies (i.e. Mayo, MGH, BWH, etc). I'm not sure if it would have helped, but I wish I took a look at their match list during interview day.