As someone who is also considering these 3 schools, here is my current take on it (though it changes pretty often). And I would definitely appreciate other perspectives that could help change my mind:
Curriculum: All pretty similar (hybrid lecture/small-group style with minimal class-time hours and more reliance on independent, self-directed learning), assuming that Emory's under-construction curriculum follows suit
Hospital Affliations: I think Grady and Case's multiple affiliations (Univ. Hospitals, CCF, Metro) have a slight advantage over NMH. I've just heard wicked things about the experience one would get at Grady, and Case seems to offer the best of all possible worlds. If you're looking to serve a heavily under-served population, I think Emory and Case inch ahead of NU.
Grading: Case is pure P/F (no rankings), Northwestern is P/F (I think they might be internally ranked), Emory is ABCDF (unless otherwise modified). HUGE advantage to Case and NU, in my naive opinion.
Cost: I think all 3 schools are in the same range (very expensive), but cost of living goes Chicago > Atlanta > Cleveland.
Location: With that being said, I think pure location enjoyment also goes Chicago > Atlanta > Cleveland, though I have friends in all 3 cities that defend their respective homes quite well.
Research: Case and Emory are both implementing shortened pre-clinical years to allow for research endeavors (or other degrees too). Case has a mandatory research "project", Emory maybe doing the same. NU does not require it. If you're into research, these might appeal to you.
Other "perks": Emory has CDC, American Cancer Society, Carter Center, Rollins School of Public Health, and they just built a huge new med school building. Case has a pretty bomb-a$$ affiliation with CCF, which I heard can be a potential boon if you make strong connections there. Northwestern lets you dual-degree with Kellogg, one of the top business schools in the nation (#1 a few years back), and you can see all kinds of star athletes when the Big-10 powerhouses come to Evanston.
I'm sure there are plenty more nuances between the schools, but I am currently viewing the 3 as very similar (academically speaking, minus the grading options), in that location might be my deciding factor. Hence, I'm leaning toward Northwestern. But ask me again tomorrow, and I might be singing a different tune. Bottom line: You can't really go wrong with any of these 3, your education will be great no matter what. At least, that's what I keep telling myself as I try to decide😳