BCM students still rotate through Methodist, so the split (that happened in 2003 btw) does not affect med students at all--but it does affect residents.
Regarding the rankings--there was a long discussion about this in the BCM forums--essentially nothing substantive changed at Baylor, but the administration decided not to report MD Anderson's NIH funding (150million) to US News along with their own (and since US News is heavily based on research funding, BCM's ranking dropped)..so nothing really changed. That being said the Rice merger will surely boost the rankings and when BCM gets a new President (sometime soon) he might make a different decision re: MD Anderson.
In any case, the point is that nothing really changed at BCM with respect to the quality of the program or opportunities for medical students. Personally, I would choose BCM--the 2.5 yrs of clinical rotations mean that you get a lot of time to try out any rotation (at phenomenal hospitals in the TMC as well as abroad, at away rotations, etc) or simply take some time off and travel/relax. Plus, the cheap tuition means that you start out in significantly less debt..it's a win-win!
By the way: speaking of the hospitals; both UCLA and BCM have phenomenal hospitals, but one of the advantages of BCM is: not only do you have great hospitals in EVERY specialty, but it's not the same hospital(ie MD Anderson for Cancer, Texas Childrens for peds, Menninger Clinic for Psych, etc)--so you have the opportunity to experience top-notch clinical care/technology but you also get to experience different hospitals, different charting systems, etc--which will definitely allow you to adapt more readily and expand your skill set in residency and beyond.