Enterprise getting messed up does not count as enterprise getting destroyed. So for the TOS movies, only 3 have those cliches: Wrath of Khan, Search for Spock and Voyage Home. And at the time none of them were cliches so they work fine in those movies. But when you re-use them again and again it gets boring. The last 4 Star Trek movies have all had revenge seeking baddies (Nemesis, 09, Into Darkness, Beyond).
They need to come up with more interesting stories. Star Trek VI has aged the best of probably any of the TOS movies just because the story is original and done very well.