As far as not being well prepared for rotations after doing your PhD, it depends. Many programs are now encouraging MSTP students to stay active in the clinic during their research years to eliminate this problem. They also have refresher seminars and such to prepare you right before you return to the wards. And in a way, MSTP students have an advantage over their MD counterparts in the wards, because they have developed their scientific thinking and questioning skills, which can give them great insight into the clinical problems they encounter.
MDs will tell you that you dont need an PhD to do research and PhDs will tell you that you dont need an MD to do clinical research or work with people. If you want the real deal on MD/PhDs, however, you'll have to talk to real live MD/PhDs. Don't only isten to others' opinions, though, do what you think is best for you. If you want to make research a big part of your career, and want to compete for top positions in academic medicine, the PhD may be worth it. You will probably also be better prepared to run a lab, if that's one of your goals. However, if you are instead concerned about the time it takes to do the MD/PhD, and have other things you'd rather do with the time, or if your reserach interests aren't as great, perhaps an MD only is best for you.
BTW, I'm applying this cycle, and currently interviewing/deciding. Myself and others here will be glad you answer any questions you have, and feel free to PM me.
