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I have loved Plusle since elementary school, but it is pretty underwhelming to battle with, and most people just prefer other Pika-clones.
I also like the Mightyena and Delcatty lines because while they are generic and forgettable to most, they are good puppos and cute cats for me, respectively.
All of these are mostly because of my (surprise surprise) love for Hoenn and the sentimental value they have for me.
I think Zubat is Pretty unpopular because of it being so annoying but in alpha sapphire I did a solo run with it and it was weak I didn't even evolve it into a golbat
but when I finally beat the game with only a zubat it always had a special place in my heart also that zubat was level 100 before I got to the elite four because I knew I was going to lose if I my zubat was only level 60.
Stunky/Skuntank. There's a story behind this. A few years back I bought a used copy of Diamond. When I checked the file it was obvious there was a lot of Pokemon with a lot of dumb names on it. One was a Skutank named Bad Purple. I used it on my team for a while and grew attached to the guy. He made me really appreciate Skuntank as a Pokemon because he became one of my best team mates. I transfer it over to White version and I still bring him out cause I've bonded with the guy so much. <3
Farfetch'd : It has crappy stats and people doesn't like his design. Even after overhaul in attack stat it was still mediocre that a lot of guys didn't use it. For me myself it's kind of endearing somewhat and i wish it get a better overhaul or evolution in the long run
Eelektross, Vanilluxe, and just a lot of 5th gen guy. And Maractus especially. Poor thing gets so much more hate now with the "not every pokemon is someone's favorite" argument going around