Do you have any support for your statement?
The WOW factor. Better research, better facilities, better training hospital. Also, Philly has too many medical schools (some, like Penn, are much more highly regarded than jefferson, and all your aways within the city will have preference for those students--from what I've heard). Step 1 scores for Emory are also higher.
Imagine if you're Jabari Parker, and you're choosing where you wanna go for college basketball. You could choose BYU because you're Mormon, or you could choose Duke/Michigan State because you wanna win. Technically, Jabari should be able to succeed under both programs (ultimately go to the NBA), but Duke/MSU will provide the best chance for him to do so (under the brightest lights, biggest games, and biggest conferences).
^^replace Jabari Parker w/ MIKEYmike1
replace BYU with Jefferson
replace Mormon with 'wanna stay in Philadelphia'
replace Duke/MSU with Emory
replace NBA with 'residency of choice'
I know that analogy has a lot of holes, but that's how I would look at things.
Emory also has strong national recognition so you shouldn't have a problem getting a Philly residency.
Also, take what I have to say with a grain of salt, because I absolutely LOVED emory when I interviewed, and am very envious that you've been accepted. To me, the decision is a no-brainer, but i'm only a senior in college!