I am in a somewhat similar situation, having been admitted into Case Western's MSTP as well as CCLCM (although my "MD-only" option is MD-with-a-year-of-research). I am leaning heavily towards the MSTP because, let's face it, MD/PhD is what I've been working for during the entire application process; however, I was really impressed with CCLCM's facilities and curriculum.
I am re-visiting both programs (to some extent, since they overlap) because I cannot, in all fairness, disregard CCLCM at this point-- it has a research component, and I don't yet have my aid package, so for all I know it might not put me in too much debt. I feel like I would be a good fit there, an opinion which is corroborated by the fact that they admitted me directly (no waitlist!). On the other hand, I think I would really enjoy being a graduate student, so the PhD is enticing, as is the thought of having a community of MD/PhD peers in the MSTP.
So, PMD, to answer your original questions: yes, I'm trying to decide, and although leaning toward the MSTP, I'm going to spend as much time as possible talking to current students with each program, figuring out where I fit the best. I have had difficulty defining criteria, since many of them involve projecting where I want to be 5 or 8 or 20 years from now, and guessing how each program will help me get there. I can't do this for myself without making some wide generalizations, so I think the best criterion is to determine which educational setting (MD or MD/PhD) I will enjoy most. The admissions process (hoping for an interview, prepping for the interview, hoping to hear back, sitting on the waitlist) has distanced me from the whole idea of what I will be doing once I actually begin medical school, and I am counting on the re-visit to give me an objective look at both programs.
Good luck with your decision! I hopefully will have a matriculation sometime next week, since the Case/CCLCM revisit begins this Thursday...