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Sorry for being a Specialfag, but I find a lot of characters in Pokemon Adventure/Special to be better than their game counterparts. Even the villains.
To list my favorites:
>Giovanni
Games: Abandons his kid and goes into hiding
Special: looks for his son for 10 years; finally finds him and saves an unconscious Silver from burning alive in the raging inferno of a crashed airship
>Wally
Games: Shows up and becomes rival right the fuck out of nowhere; respectable for overcoming his disease, but very random kid in the grand scheme of things with no connection to plot
Special: Climbs Sky Pillar despite his illness and teams up with Norman to awaken MOTHERFUCKING RAYQUAZA to save Hoenn from being destroyed by both Kyogre and Groudon
>Gold/Ethan
Games: beta faggot if NPC; defeats Elite Four and Red if protagonist
Special: straight up baller; rides a skateboard; has a MANTINE SKYGLIDER; has the title of hatcher/breeder; has the best Togepi; does things usually for shits and giggles; just a fun guy to be around
>Green/Blue
Game: pretentious whiny douchebag who can't admit to his mistakes until the end; becomes tolerable as a gym leader
Special: Calm and collected and shits on Red when they first meet; arrogant but skillful so you can't really mess with him; has his Charmeleon slice a fucking Arbok's head off without so much as flinching; becomes one of the biggest bros in this manga
And don't even get me started on the gym leaders...