Is it generally acceptable to use your favorite Pokemon as the main characters Pokemon? (With out it seeming to degrade the story.)
Why would using a particular Pokemon
degrade the story?
Let's take me as a good example. I love Pikachu. I think that the rat is cute, adorable, and huggable, especially when nicknamed after certain science fiction characters. I like Pikachu so much that I plan to write one into one of my fics. Does having a Pikachu make my fic any less of the quality it would be without the Pikachu? Not really. The story might be different, but it's still going to have the same quality. I have the Pikachu in the story because I want to write about a Pikachu, just like I want to write about the Rattata character. I picked Pokemon that I want to write about, and some are also my favorite Pokemon.
But the story is not "degraded" in any way. It just means that my characters have Pokemon that I like, or at least have some interest in writing. I'm not going to force myself to write about Pokemon that I either don't like or have no interest in writing just to please the readers. They are reading the story that I wrote, and I want to write about Pikachu.
There shouldn't be any serious repercussions using a particular Pokemon in your fic. (Within reason. I mean, don't just hand your character a Legendary Pokemon and lol your way through the story.) So what if you want to hand your trainer a Pikachu/Lucario/Garchomp/Infernape/Tangrowth? Just as long as there's a good explanation as to how the character got it (no starter Eevee, please), then it's fine.
It sort of sounds like if a writer uses their favorite Pokemon, then it's an insult to the fic. Which is a rather hilarious idea to me. I guess that this idea that you can only write about certain Pokemon so that your fic isn't "degraded" is a bunch of something.
(And yes, DP479, I was thinking of you during this post, and your hatred of Pikachu.)