To answer your question too late...
Having just graduated from BCM and doing oto, I can answer your question, albeit too late for you. First, the new hospital won't be open until 2010 at the earliest. The first phase of the hospital will be small, 250 beds or so. The OR space will be mostly for general surgery use, with all the surgical subspecialties sharing OR space and time. Considering the Neurosensory center at Methodist runs 4 or more ORs full time five days a week, which are majority used by BCM faculty and a few private folks, sharing an OR for a few days a week at the new hospital isn't even close to enough to keep up with the faculty now. If anything, the Methodist contract could and probably should be extended beyond 2010 until a full suite of ORs could be assigned with enough room for all surgical faculty full time 5 days a week. This would happen during the second phase of the hospital. Until then, probably small consult service and shared OR time when the hospital opens. The department hasn't made any plans that I'm aware of (I'd ask current residents). Considering you're graduating in 4 years, the new hospital probably will be open for your clinical rotations and it might change surgery or medicine rotations, but won't mean much change for the Baylor oto program or you in regards to oto apps. But for the future and what the hospital means, it means change. At this point it's impossible to tell if the new hosptial will be the better or worse for you, the department, or Baylor in general, especially because it will not be at full power just yet.
That said... DO NOT DISCOUNT THE POWER OF THE 18 MONTH BASIC SCIENCES. It will be your best weapon for preparation for Step 1. Last year's avg from BCM was around 237 because we are able to put a lot of effort into studying. The faculty, attendings, prog. director and residents from BCM are first-class and will give you great advice if you ask in time to put it into action. Your dean's letter also comes from a respected oto faculty. I've heard some people refer to Dr. Alford as a dinosaur, and if that's true, then that must mean that dinosaurs are benevolent, extremely knowledgeable (always get your name right), connected and powerful, and yet genuinely nice creatures who do not raise their voices.
Lastly, you also have the opportunity to do research at BCM (mostly otology) or at MD Anderson in head and neck. It's like having another awesome 10-person faculty and tons of labs for you to interact with.
This year's BCM oto applicants were as successful as in the last few years and, in my opinion, awesome people who ended up very happy with match results as a group.
So I hope you went to Baylor.
Thanks for your input guys. It seems that the new hospital at Baylor is not an issue. Both schools seem to be awesome and I feel fortunate to have this choice. Only two weeks left until the decision deadline...