Thanks for your questions! I won't be able to answer the MS3 one (since I have so few data points), but I have a good idea about the rest of them.
What are pros and cons of Yale, besides Yale System?
For the record, I think the primary aspect of Yale that applicants should consider revolves around the Yale System. The first question you should ask is whether you've been craving an unprecedented level of freedom and independence in crafting your medical education. Some people thrive in this sort of environment (like myself!), while others feel like they need more structure to do well. Your answer to this should be your first (and most significant) consideration. Otherwise:
Pros:
The most important ones for me are the small class size (100 students), optional tuition-free 5th year for research or dual-degree programs, MASSIVE international health opportunities, established free clinic, and the fact that the medical curriculum makes it a point to make all of the other resources in other departments available to you. I'm someone interested in developing medical devices for the underserved, so the flexibility, mentorship, and resources offered are exactly what I need.
This might also be helpful:
http://medicine.yale.edu/education/admissions/education/63955_med_100805_web.pdf
Cons:
Cold. Cold cold cold cold cold. I'm from places where there are only two seasons (summer and hotter summer), so I freely admit that the snow will be an adjustment. There are also comments about how there are parts of New Haven that experience higher crime rates, which can be a concern for some students (although will be an issue if you go to any medical school in an urban area).
How are schedules like? Are afternoons mostly open like the schedule at Case?
So for us, we'll get about 3 afternoons completely free a week for the preclinical years. I've heard (unofficially, someone will need to check me on this) that for you guys, they'll be shifting to a 1.5 preclinical + 2.5 clinical model like Columbia/Penn, and I'm not familiar with whether that will change what the schedule looks like.
What does Yale look for particularly in applicants, if any?
Fit for the Yale System. Obviously you have to be academically capable and well-rounded, but you have to demonstrate a certain extra level of independence. Use the "Why Yale?" question to your advantage! I'm confident that's what got me my interview.
Describe your interview experiences at Yale.
Most relaxed interview experience of my cycle, hands down. There were something like 12 interviewees my day. You arrive in the morning, meet with Director Silverman, and get your interview packets. We sat in on a medical ethics class for an hour, which was wonderfully fascinating. This is also your chance to get candid feedback about Yale from current students you meet during the class. There's a financial aid/curriculum talk in the morning, you have lunch with a faculty member, and there's a student-led tour of campus.
There are two interviews (1hr each) either at the end of the day or sprinkled between the morning (11-ish) and the afternoon if you have flight schedule constraints like I did. As with any interview, every experience is different, but I can say that mine were as relaxed and conversational as they could possibly be. Neither of mine elected to take any notes, and we just
talked. It was wonderful. One heard me talk about my interests and offered to get me in touch with a faculty member, and she followed-up the next day!
How easy and encouraging is Yale in terms of doing research as MS1?
I'll be able to give you a better answer in a few months, but I will leave an anecdote my student interviewer shared with me. She is currently a 3rd year (taking time off after 2nd preclinical year to do a PhD at Yale), but she took complete advantage of the curriculum's flexibility to pursue her interests in research as an MS1. She basically just didn't attend classes and spent all of her time in lab, pumping out multiple publications her first year. She got back into gear, buckled down during the Step 1 study period, and still dominated boards.
Obviously this doesn't mean you have to do this level of research as an MS1, but it suggests to me that it's enormously easy to get involved.