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I really can't pinpoint my favorites because they change so much, and they really don't have a backstory because I usually just like them because they're them.
But one pokemon that's always stayed on my top 5 list is shiny mightyena. Caught one in an emerald run. She was brave, my favorite nature (>not using natures to describe the pokemon's personality), and stayed as a main and independent teammate through the elite four. She never fell behind and since then I've always loved her.