I think the top reason that DOs choose to do a MD residency vs. a DO residency is that there are many more MD residencies. Thus, you have more control in terms of where you do residency. Those in my class that have applied for the DO match usually do so for the transitional year, before they begin their specialty training through the allopathic match. Being able to do an osteopathic transitional year is a significant advantage in CA because there are so few spots available in the allopathic match.
Other reasons include the opportunity to do residency at say UCSF, Stanford, Yale, Columbia, etc... I am only citing reasons that I am aware of in my class, I can't speak for everyone else.
Which match you do is ultimately up to what you want to do with your career. Some DOs who want to do FP or Ortho Surg, find the additional training in OMM and muscloskeletal medicine to be a very valuable asset. Those that decide to do Radiology, Neurosurgery, General Surgery, or Emergency Medicine are more like to try to go through both matches until they land a spot. Some people want the prestige of having gone to a place like the Mayo Clinic, Harvard, Hopkins, etc...
I wouldn't say there is a significant advantage to either. Both will teach you what you need to learn and provide you with the license to practice in that field. If you want to subspecialize in IM, I would recommend trying to get into a prestigious program that has fellowships in the field you want to go into.
All in all, I would say that the top reason to completely bypass the DO match is due to location. More and more programs are becoming dually accredited now. For example, it is widely known that to get a residency spot at one of UC Irvine's affiliate Residencies in either the transitional year or the Family Practice residency, it is easier to go through the DO match. They offer spots through both the Allopathic and the Osteopathic match for the exact same residency. The degree and the residency are exactly the same. Additionally, if you fail to match through the osteopathic match, you can apply again though the allopathic match. I can't remember the other schools that have this same situation but the numbers are increasing. I saw a list posted on one of the threads on SDN. Hope this helps, and don't worry about the match yet. You've got plenty of time.
