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3 >4 > 6 = 5 >1 > 2
Gen 3 holds the fondest memories for me since it's the gen where I found my first shiny pokemon (I basically skipped from Blue to Firered to Emerald, so I never got the red gyarados in GSC), it's also where I leveled up a pokemon to level 100 for the first time (my blastoise in Blue would've been that pokemon, but I got tired of using it around level 87ish). I've also had some of the best moments playing it with friends because it's the first gen where my friends and I all had the same system and type of games, so I bought a link cable and we constantly battled and traded with each other (they didn't get GBCs, so we never played Red or Blue together).
My favored companion is probably my favorite pokemon: manectric. I actually have a female manectric in my Y version named Lupa that's always in my team.