A big difference is that at NJMS -- the students are in the same phyiscal plant for four years -- pretty much. At RWJ, 1/3 class goes to Camden and the others go to RWJ-UH which is also not near the basic sciences classroom.
I'd think you get to see 3rd and 4th years a bit more at NJMS. Could someone at RWJ post and say if that's true there or not?
And, yes, NJMS does have some organizational problems. But, the new Dean of Education is really on top of things. And, students are very motivated in terms of clubs, bringing in speakers too.
Look also at how many people are in each place -- 170 at NJMS 150 at RWJ -- it's only 20 people but it can make a difference if you want a smaller or larger class.
If you want go to:
http://catalyst.umdnj.edu/plexus/ -- NJMS's online version of their student paper. You can get a good feeling for the pros and cons of the place there.
In the end though, I feel you have to listen to your gut. It's a tough decision. And, yes, I would say too that RWJ gets more applicants to come there over NJMS who were common acceptances. Their admissions staff is awesome. And, the facilities are superior to NJMS.
But, neither school is going to hold you back if you really put all your work into it -- look more into the environment -- and, at this point, curriculum differences.