Quite often their is very little difference in the way that an MD and a DO practice medicine, other than the addition of some OMT by some(not all) DOs.
As they said, it is MUCH more dependent on the person, not the letters or school. Many MD's are greater than some DOs, and many DO's are greater than some MDs. As far as reputation goes, it is somewhat still dependant on location. The further you look East and North, in general, the less problems you see with respect and recognition. Here in Michigan, there are honestly just as many DOs and MD's, and their is never any question, competition, or adversity between them. They are virtually interchangeable. Many of them practice together, it is very easy to find a family practice partnership with an MD and a DO together, or a mixture in large practices. I work for an urgent care center that is owned by 7 DOs, and 6 MD's. I have never heard a doc or a patient ever question what a DO is, their competency, their ability compared to an MD, in fact, I had never even heard them compared or looked at as "lower" than MDs until I got into the premed thing deeper, talked to people from out west, and joined SDN. Anyway, from what I understand, as you look, in general, further west and south, you find a bit more of the question or negativity towards DOs. I have never been to such a place, but several SDNers are from out there and can better describe and verify the condition out there,
It is getting better, and there will come a time when DO bashing and questioning will be history. DOs are constantly proving that their education is NOT substandard. In fact, over the years, DO and MD practice seems to be getting more alike than different. If you were treated by 20 docs, 10 MD and 10 DO, eliminate OMT and the letters after their name, i bet few people would be able to identify which were which beyond guessing.
Residency should be a factor in deciding. While DOs are eligible for MD residencies, it is more challenging to get them. First, DOs usually take a different, although similar and equal, licensing exam than the MD USMLE. However, if a DO wants an MD residency, he/she will almost always have to take the USMLE as well. Not a problem as far as education goes, but the USMLE is different, and after taking one stressful license exam, studying and taking another will be that much harder. Many of the things you use for those type of exams may be the "forget it after the test" type of thing, and you are sure to be exhausted after studying for one exam alone. I am a paramedic, and while my licensing exam is hardly comparable to a docs, I can tell you that after one day of testing for my state license exam, it would have been really tough to take another one shortly after. On top of that, most DO programs are highly geared toward family practice or close specialties(like internal med, peds, ect.). If you plan to take a specielty like say neurosurgery, you may want to investigate which programs best suit your goals. Not to say the DOs can't do that, I work with a DO neurosurgeon at the urgent care.
Hope that helps, ask more ? if you have them or need more clarification.