Ppl here are arguing over something OP did not ask for.
OP, straight to the point, you want ortho, correct? You'll have to fight for it and prepare to work your ass off from day 1. Neither of these schools can give you ortho, it is up to you.
From an inside source by a senior ortho resident, only 1 DO matched into ACGME ortho program in 2014-2015 cycle. This cycle is even worse -- one MD student with research experience + published + ~240 on USMLE 1 + high pass on away rotations DID NOT receive one interview invite before Thanksgiving, this person probably received some after Thanksgiving but the chance to match is low as the cycle is very competitive b/c multiple applicants go on more interviews and don't cancel any. Therefore, your chance lies more with future ACGME accredited AOA programs. AOA programs split into two types: Board heavy or IDGAF about your boards -- there are more board heavy programs such as Des Peres, Toledo, Doctors, Harrisburg, Broward, Corvallis, etc. So really, it only comes down to your boards score if you truly want to be competitive. I'm not talking about 500s or 600s, but 700s range on the COMLEX. No surprises there, the most competitive students would gun hard for the highest board scores. Face time is very important in AOA programs, you'll have time to do away rotations with both schools. Onto research opportunity, we're not talking about just any clinical research here, but specifically ortho. As aforementioned discussion above, neither school has any active ortho research going on, so you will have to reach out to close by institutions. You won't get any research at MUCOM. IU students will be preferentially given the work before you and guess what? There are over thousand IU med students. They will get hooked up with any ortho project before you can cold call and get your hand on one. You'll be more likely to get research with BCOM via affiliated state university. One thing I'd like to point out, MUCOM is notoriously well known to push for primary care as it is the school mission. Based on that and other mentioned presentations, I'd take BCOM if I were in your position.