Honestly it comes down to the class structure. The people I'd most want to rotate/work with would be at SKI anyways, so I don't miss out on professors at Weill, Rockefeller or HSS, so that doesn't really matter. I don't care a whole lot about the larger university community that's available at Weill, and I actually like the idea of being a tight knit cohort. Working as a technician right now at CUMC, I see the rotation students constantly running in and out of lab in order to be in class and do homework. That is not something that I'd want to do, and the GSK program where rotations and classes are separate avoids it. Also, I'm pretty sure the ACE for GSK is your thesis presentation, as opposed to something unrelated.
TLDR: Research is the same. Stipend is the same. Housing is the same. Classes and rotations are separate at GSK.