I'd say the fact that Duke has gone to the new model of the shortened preclinical MD track is a very powerful pro due to the ability to do clinical work prior to the PhD, if that matters to you. Makes the first year of MD super intense but you do get to graduate a year earlier. Whether that *actually* makes a practical difference is debatable and there, to my knowledge, has not been an indication that this change has led to a statistically significant difference in Step 1 scores or match results (at least at Vanderbilt the same model has not seemed to change very much), but what struck me is that you seem less enthusiastic about the non-Duke options due to the dearth of ophtho options. 1 PI in your field of interest isn't ideal. You don't want the fact that you don't vibe with your only possible mentor to be the reason you switch research interests.
But I guess that's what second looks are for. Meet the PIs that you're interested in and see if the fact that there are only a few potential mentors at the non-Duke options isn't actually as much of a con as one might think. Perhaps a co-mentorship with an ophtho PI and a basic neuroscience PI might defray potential issues there...see how encouraging each of these schools are of co-mentorships etc.