The only negative things I have heard about Baylor are:
(1) The MD/PhD program will not "grandfather" MD/PhDs in when they return to the MD portion of the program after getting their PhD. (Any course changes that occur while you are in the program you are subject to.) This means you may have an extra course or two that you weren't anticipating when you started the program and you might have to stay an additional semester. Pros: Get an up to date medical education, more time in clinics before Step II Cons: If you try and get some class out of the way before entering the PhD part you might end up taking a class that will no longer be required or completely fulfill a certain requirement.
(2) The split with the Methodist Hospital (formerly one of Baylor's primary teaching hospitals) was really nasty (you can search
www.chron.com for articles from the Houston Chronicle about it). Unfortunately, a lot of faculty felt like they were being given an "us or them" ultimatum and a number of clinical and research faculty left on less than amicable terms. No idea how this affects clinicals; Baylor has partnered with St. Luke's instead.
Overall, I love Baylor and would go there in a heartbeat. The med students I've talked to say that everyone is friendly and helpful as opposed to competive. However, sometimes it can help to know exactly what you are getting into.