I am sorry to hear your story of a 12 year MD/PhD. Your program director was ineffective. One of the main duties of the MD/PhD program director is to keep students on track. To do that, you do not only need to keep meeting students often, but also to be brutally honest about their advancement and prospects. The PD also needs to have a lot of cloud in campus to help students get out of a bad situation early enough in their training. In my program, all students are formally reviewed by an independent panel every 6 months. In addition, I meet with them individually every 6 months and twice a month in small groups. We also require a F30/31 submission within first 18 months of PhD work. If the study section raises questions about the mentor and/or the project, I meet with the student and mentor individually. In at least a recent case, I enable a student to leave the lab of a basic science "chair" after 1 year because of these concerns, and help her get into a lab where she is now making considerable progress toward her project. One of the key aspects of getting into a MD/PhD program is the commitment and quality of your PD.
Obvious commercial... Look forward to your applications for the 2014 cycle. Congratulations to those interviewing these year.