It's one of the better movies, but far from my favorite. I prefer Voyage Home, Undiscovered Country and Into Darkness on (my subjective assessment of) objective grounds. I freely admit that Final Frontier is of inferior quality to Wrath, but I'm still more likely to watch Final Frontier, because it's more fun.
The first time I saw Wrath of Khan, I actually didn't like it at all, because I felt like it didn't do justice to "Space Seed," one of my favorite episodes. I'm not talking about continuity or accuracy issues, at all. Thematically, I liked the way "Space Seed" ended, with mystery and potential for some new kind of human society, and I didn't like how Wrath short-circuits all that. Plus, Khan is so clever in "Space Seed." He arrives in a position of complete disadvantage and almost takes the Enterprise. Contrast that with Wrath, in which he falls into a position of complete advantage, entirely by luck, and Kirk systematically erodes that advantage. I'm laughing at the superior intellect right along with Kirk. But over the years, I've come to appreciate Wrath of Khan for its own strengths (it has them in spades), apart from my feelings about "Space Seed."