And while we're on the subject (btw, this is one of the things I like to rant about, so be it over thine own head for bringing it up), it makes me grind my teeth whenever I see people say things like, "Well, I thoroughly enjoy twisting the cliche when I write my story."
You don't twist cliche. If you put a new spin on an old idea, it's just that; it's not taking a cliche and suddenly making it "original." Take, for example, the cliche of the "waking up to get pokemon." This is a cliche--it is a device used so often that it no longer has any excitement, mystery, or suspense associated with it. Now, some peole may say that their story starts out this way, but is not cliche because of other things that happen after it or because the way that the wakening is presented.
This is not true. You either have the character waking up on the day that they are to get their first pokemon or you don't. If you do have this and even if the rest of the piece does not even remotely resemble the "generic" journeyfic, the opening scene is still not a cliche, but not the entire piece. Opening your fic at a different point or scene entirely is not a "spin on the old cliche" but rather a different way of going about the story altogether. One does not modify a cliche to suddenly make it a non-cliche; cliches are very specific things, but people often apply them too broadly. It's not "sort of" cliche or "mostly" cliche: it either is or it isn't.
By the same token, OT stories are not cliche. They are a legitimate genre of fanfiction with their own generic conventions. Calling an OT story cliche is like calling a mystery cliche "because come on, every mystery I read is about somebody having to solve something." That is a generic convention of the mystery genre; the generic convention of an original trainer tale is that it involves a non-canon character who is a trainer of pokemon.
The OT genre is so often labeled as cliche because it has its own unique set of cliches that are easily recognizable to most readers. One of these is the "wake up, get pokemon, get outta here," scene. Another is the "oppressive parent refuses to allow child to leave on journey" plot device. No matter how you twist it, your story either includes this or it doesn't. If it doesn't, it's not some wildly original take on a cliche, but a different idea entirely. If it does, then boo-hoo, it's cliche. Deal.
About the only way to put a new spin on a cliche is through parody or humor. Poking fun at cliches by using them in a piece is examining the cliche and exploiting its weakness. The cliche remains the same, but the intention of it is different.
The danger that you run by using a lot of cliches is loss of impact with the story. Basically, it's a "been there, done that" effect. Cliches are so familiar and habitual, however, that they can also be used to harbor familiarity and comfort with a particular scene or character. They're something that readers will instantly recognize. They cannot hold up a story on their own, however. While in general it is best to avoid them wherever possible, it is not the end of the world if you use some. Your best bet is to be aware of what your cliches are, and consider whether they serve the story best or if they are merely a symptom of laziness, using a tried-and-true formula to approach your writing.