Wrath of Khan was the best Star Trek film ever made period. Now I've barely seen any other ones except for the newest ones and I enjoyed the 2009 Star Trek I'm not sure why I even invoked it in the above (although I'm not sure Trekies liked it very much). But Star Trek Into Darkness was .
I'm not even a Star Trek fan at all so I care very little to compare the older films to the two new ones. I only take these two on their own and will not even consider detracting it based on things from the show or other movies.