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I try to give my Pokemon a reference name that isn't too obvious, but relates to something.
I started with a froakie named Glenn. I eventually wasted a ton of time breeding a shiny Froakie with Protean... and I don't know what the odds on it being all three are, but she turned out to be shiny too, so I named her Tiana (and not just because she's black).
My first Hawlucha was named El Topo Chico after a character in a funny internet video I saw.... and when I bred a shiny of that too (I have a lot of free time), he was named Ocho Muerte... after a character in a different funny internet video.
Then there was the Honedge, which I called Mune, which I used to breed a shiny called Mura.
I picked a bulbasaur as my gift pokemon and named him Onion, specifically after the Steven Universe character. He made it to my first Hall of Fame, though I pretty much haven't used him since.
A friend of mine bred me a Charizard and I asked her to name him Cole, 'cuz, y'know... coal. Later I traded a non-protean shiny froakie for a shiny Charizard, and while Cole is a much better name for him it was a trade, so his name is just Charizard and I've just gotta deal with that.
The rest of my team I actually made out of folks from Wonder Trade... so nothing really creative to do with them. If I feel like throwing away another 5+ hours of my life I might breed a shiny Tyrantrum and name him Koopa... specifically after President Koopa from the Super Mario Bros. Movie.
No idea what I'd name my Gyarados if I could... maybe just Danny Trejo, because of his bitching mustache.