(Sorry about the tl;dr, but I felt like fleshing out the reasons I chose these 3 a bit more for anyone who's interested)
1) Vaporeon (so useful for both competitive and in-game use... but the reason he's my #1 vote goes far beyond that. I didn't even care for it all that much when I was a kid. But it grew on me so much as an adult a few years ago when I played through Gen 1 again for the first time in well over a decade. I know it sounds stupid, but the bond I had with this little guy during that playthrough, growing him from a little Eevee into a powerhouse helped me remember why I loved Pokemon games to begin with, and made me want to just play the games again instead of only focusing on competitive battling. Pokemon were a huge part of my childhood and I have so many memories playing Pokemon Red on my Gameboy Color raising my Pokemon all the way to level 100. When you decide to take a Pokemon with you on your journey and slowly raise it from being a little weakling you grow a bond with that Pokemon as it gets stronger and stronger and becomes better and better. Vaporeon helped me feel that bond again for the first time in years and for that, it holds a special place in my heart)
2) Mewtwo (His visual design is great, he's incredible competitively especially with his new mega forms, and he has that nostalgia factor as well. There's just a dark vibe to him and the lore surrounding him is unmatched by any Pokemon. He's a clone created by humans who's even more powerful than the original, but learned he was a clone and became uncontrollable and destructive towards humans. He destroyed the lab in which he was created and likely KILLED people. But you were the one to beat the Elite 4 and become Champion, and as your reward you are able to traverse through Cerulean cave and find Mewtwo, the most powerful Pokemon in the game. He was the original powerhouse you saved your masterball for. And the fact that he's still one of the most popular Pokemon to this day even with all of the other crazy good "uber-tier" legendaries out there just shows that he's arguably the BEST Pokemon GameFreak ever designed. While many Pokemon such as Charizard's popularity rides simply on the fact that it's a fire breathing dragon and was a lot of people's first Pokemon, I feel Mewtwo's popularity actually has a deeper story behind it. He's not JUST a Pokemon, he's a character)
3) Ho-Oh (IMO best shiny Pokemon of all time, easily one of the best legend themes in the games, great and versatile competitively in Ubers play. Ho-oh always had a mystique to it being the first legendary ever shown in the TV show before we, or Ash's Pokedex, even knew what it was. And it was the only Pokemon to know the badass move Sacred Fire until Entei recently got it. I played the hell out of Pokemon Gold as a kid and Heart Gold was the first Pokemon game I played as an adult so there's just a certain nostalgia about making your way up that sacred Tin Tower and catching Ho-oh. That scene of Ash catching a glimpse of a glowing Ho-oh soaring through the sky leaving rainbows behind it in the first episode of the anime will forever be engraved in my mind)
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