Three Yale grad schools top U.S. News
"Weakness" at YMS is in clinical departments. YMS's basic science departments have always been world class, and its clinical departments used to be among the best too. However, in the past 20 years, clinical departments have clearly experienced a "reputation" decline. "Higher ranked" schools like Harvard, Johns Hopkins, Penn, Duke and Wash U tend to have clinical departments that have more robust basic science enterprise than Yale's. In addition, a big disadvantage that YMS has in comparison to others is that Yale-New Haven Hospital has a "split loyalty." In other words, half the doctors who admit to YNHH are private practitioners who have little interest in seeing Yale improve and advancing clinical sciences. As a consequence, I don't see Yale-New Haven as a magnet for advanced patient care like JH, Partners, Cleveland Clinic, or Mayo Clinic.
Yale Med is infinitely more respected than Harvard. As the Dean said, Yale has more money per faculty member, indicating a higher overall quality.