Can we all please chill with overwrought stereotypes of major institutions? As someone who went to Harvard for undergrad and now works in an HMS lab, and is applying for PhDs, there are great things and awful things about Harvard. Also in your stereotypes, you're making a hilarious equivalence between medical research and biological/biomedical research. It's very hard and frankly incorrect to connect research into surgery techniques to research on DNA or the cell. Also just saying an institution "was amazing in the history" ignores what it currently is, frankly when a lot of those discoveries at JHU were being made Stanford was like 20 years old, so let's all chill.
I applied to only six schools, but I applied to them because there were faculty there that I wanted to work with on topics I'm working on. Most graduate programs are defined by your PI, as I've learned working full-time in a lab the past two years. If you're just choosing for "reputation" or in spite of it, you're going to miss great opportunities.
I can tell you for certain BBS is a program that will let you do anything you want pretty much, and it is incredibly student-dependent in outcomes. In that way it's similar to the Harvard undergrad experience. But the idea that you're just a PI's bitch or not doing good science... you literally can't make such broad statements because every lab is different. Let's chill with overgeneralization plz.