Are you IS or OOS to West Virginia? That will play a large role in your admission to either institution.
Marshall is a small class (~75) while WVU has a larger class (110-120). Admissions to WVU is more competitive (higher AVG GPA, they both have lower MCAT averages - but WVU has stringent standards for OOS, Marshall has higher OOS standards too but might be flexible since they are friendly to nontrads.) I think slightly moreso with Marshall, you need to have ties to WV to be competitive at either school. Both appear to have more traditional curricula - mostly lectures with some small amount of PBL stuff. Other than that, the big difference is going to be Morgantown or Charleston (WVU) versus Huntingdon.
As an OOSer w/lower GPA, I got rejected from WVU immediately but the Marshall adcom has been incredibly friendly and helpful through the process for me. I found that I prefer them for the smaller class size and I've heard lots of good things about getting great clinical opportunities during third and fourth year - I am really excited to visit in a few weeks!