First and foremost I would consider where you could see yourself happy for the next three+ years. My impression has definitely been that all of the different programs offer a very comparable education, aside from slight differences. What the distributed programs possibly lose out slightly with access to highly subspecialized clinical/research experiences, you can easily argue that they make up for it with smaller group teaching and more opportunities intrinsic to the smaller class and medical community at their site. The distributed sites generally seem to have a more cohesive and connected culture than the larger amorphous VFMP program (barring some exceptions), but I would argue that in VFMP you also have great opportunities to "find your people" within the larger class, and a wider range of in-person extracurricular opportunities.
Everyone has the opportunity to do the same fourth year electives, which is where one gets most of their references letters and a significant amount of networking opportunities. To be honest, I remember stressing the choice between these sites years ago when I was in the same position. If you do a little introspection and rank according to what feels like a best fit with your personality, you can't go wrong. No choice alone is guaranteed to substantially impact your career prospects one way or another. I ultimately chose VFMP, but I could have easily been happy at a distributed site.