My brother goes to Baylor as an MD/PhD student. The split from Methodist has caused him much headache, and he is very unhappy with the new administration. He feels as though they are mugh stingier and uptight. (Something about bus passes, lab time, comp drinks...) From what I gather, the split hasn't really affected general students that much, though he does comment that it has effected MD/PhD'ers.
In addition, he talked about he felt he had a huge potporri (if you will) of information, much of it very specific, and upon general application in most cases useless. When completing rounds with UTHouston kids he felt they had a better basic understanding and more applicable skills. He says 'if you want to be Dr. House, you better be going to Baylor.' But...Obviously they know their stuff, just check out USMLE scores.
Also, as it is a fabulous school with a fabulous reputation, his first few years were HARD. (What med school isn't?) I would oftentime note him saying things like, "man I wish I would have taken the MD/PhD at ____" I don't think that given the chance he would go to another institution, however. Other students are, along with being fun and well rounded, extremely bright, and he has quoted that a good percentage of his class are the very very studious, competitive type. That was very hard for him, as he was in a major in undergrad that he naturally excelled in, and now had to compete with 'people who's only social interaction is with their textbook.'
But, he also says there's plenty of people that aren't. Obviously Baylor is going to gather some very well-rounded candidates as well.