Reason the reboot comes out ahead
Part of the answer is in what Star Trek (2009) was meant to do: reinvent the franchise for a wide, modern audience while also paying tribute to the classic series. Critics liked the fast pace, easy-to-follow character introductions, and big-screen extravaganza. These are all things that work well in modern reviews and help gain a lot of "fresh" notices.
Another factor is simple timing. The 2009 film benefited from being reviewed in an era when large online outlets routinely published reviews that count toward Rotten Tomatoes, giving it a wider base of professional coverage. Wrath of Khan, on the other hand, came out in 1982; therefore, many recent reviews aren't digitized or weren't recorded by RT. A lot of its present critical footprint comes from retrospective pieces. Even with that issue, it's still one of the best Trek movies, but not the best. (Continued...)