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I've got too many favourites phasing in and out of my memory, but I have always been pretty fond of this gal.
It started in Gale of Darkness when I first caught her, purified her, and transferred her to Ruby along with a few other shadow Pokemon bros.
I boxed the others, but I don't why I kept Mawile. She wasn't really anything special, but I always found her design to be so weird and unique. It really clicked with me.
Around the same time, I was playing various Zelda games, and Mawile really looked like Medli from the Wind Waker to me. Probably because of the ponytail thing. I would name Mawile based off of whatever Zelda character I was feeling for. Sometimes she was Romani or Malon. Other times she was Medli or Tetra. When it was time for her to transfer, I just decided on naming her something unique: Mieut.
Every generation she transferred up to, I took her along in the postgame, catching legendaries and what not. She was never really good at battling, or anything.
Then Gen 6 gave me Mega Mawile and I've never seen her kick so much ass.