I know I came late, but the discussions here are so precious for me! I am also accepted to both the MARc (STJ) at YDS and MTS at HDS, and it's so difficult to choose. My interest lies in the history of the Jewish people and the Jewish religion in the Graeco-Roman period, and rabbinic literature also fascinates me (although I have never been able to read it in its original language). Consequently, I think YDS will better prepare me for a Ph.D. program in these fields. However, the professors at HDS are also great, and I do not know whether my interests will change. In addition, I am also a non-Christian, and the information in this discussion made me less worried about my religious identity.
If possible, I would really love to know how you made your choice, and how you feel about the program after a year of studying. Many thanks!