I don't necessarily think many of these cliches are that bad to use. I'm currently writing a re imagining of the Red and Blue Story line Red has a Pikachu and he also got a Charmander from oak. Similarly Blue had an eevee but also received a squirtle. As you may imagine their are cliches abound in this story but I don't think that it automatically makes it bad because it's how you use them. At the end of the day the bad guys should lose as it involves the protagonist overcoming the main conflict (of course their are ways of circumventing that but in general the protagonist should defeat the antagonist.) As for things like pokemon that never die well that all depends on how dark one wishes the fic to be, the Pokemon Anime does not have a whole lot of pokemon die(save for a few times during the movies) because it is a kids show and is not very dark. Artistic choices that make the fice more or less mature does not constitute an over used clique. I could go on but my main point is that most of these aren't over used you just don't think they should be used