Like everyone else, I faced this decision a few years ago, these were the issues that I considered. I've little doubt that subsequent posters will disagree, but, all in the spirit of good discussion...
Where the differences might be vague in some ways, in many ways the difference between the two is quite distinct, if in only subtle ways.
In terms of acceptance, which school is more difficult to get into always raises a debate. If you are looking at pure academics, you will be immediately eliminated from a large number of MD schools on your stats alone, where the DO schools might choose to "look beyond" those stats. So in purely academic terms, you could say that DO schools are "easier" to get into. "High quality applicants" are defined differently by different schools, so, if you are "high quality" but your numbers are a little low, DO schools might still have a look at you. In my own experience, I know of people who did not get accepted to any MD schools, and then chose DO as an alternative route. I have never heard of the opposite (though they may exist). Many folks claim that because there is a 5:1 ratio of DO applicants to accepted vs. 3:1 MD, that DO schools must be more difficult to get into. There are some real problems with that line of reasoning, but that's a different issue.
Now for some generalities:
In terms of education, DO schools tend to be private (and expensive) where there are many more state MD schools (cheaper).
DO schools tend to be in rural settings, where MD schools tend to be set in academic medical centers (tending to be more urban). MD schools tend to have a sub-specialty focus afforded by the medical centers associated with it (though many are primary care oriented), DO's tend to all be primary care oriented. Because DO schools tend to have no major medical center associated with it, you may have to travel all over the state/country to get all of your year 3-4 clerkships done, where MD schools have a very well developed infrastructure.
MD schools tend to be research oriented, where DO schools tend to not (e.g. despite the long history of it's practice, there is still insufficient evidence on the efficacy of many OMM techniques). I think that this is a big issue to be addressed by the AOA, and then we all can practice it in the name of good patient care, or dismiss it as innocuous.
The DO infrastructure is buckling under its own weight. There simply are not enough DO residencies to go around, so it must depend on MD residencies to train its graduates. This may mean that you will have to take the USMLE in addition to the COMLEX to participate in the MD match.
DO residencies tend to be a year longer than MD residencies. This stems from the practice of DO graduates doing a general "osteopathic internship" year prior to starting a residency. This, so I hear, is different from program to program, I don't know for sure.
DO's still lack worldwide recognition as being fully fledged doctors. This is changing, so I hear, so we shall see.
There is still a bias against DO's by MD's (won't refer to them, etc...) This will probably also change. We shall see. On the other hand, with the rise in popularity of "alternative medicine" many DO's are reaping rewards by being a little different from the mainstream.
As a DO, you will have to continue to explain what it means and that you are "just as good as MD's."
All this being said, if I was unable to get into an MD program, I too would have attempted to go the DO route. We are all on the same team after all, and I wanted to be a doctor.
Above all else, the best program is the one that accepts you. I hope this helps you.
