What's your favorite Pokémon belonging to a character in the manga or anime? I've only watched Gen 6 and a bit of Advanced, but I'm always anticipating the arrival of May's Skitty, and Serena's Eevee never failed to bring a smile to my face.
Dawn's Piplup and Buneary always was such characters, it made me excited to watch since I knew something wonderful was gonna happen. Either a laugh or cheering, I am sure I cried once her twice as a kid. I just loved their Pokémon.
I really loved Gold's Togepi. I don't think many things can beat the attitude it had. I also liked Yellow's Chu Chu, but solely because it doesn't have the heart tail that female pikachus are supposed to have. Everytime she shows up (after gen 4) I look and see that, yup, they still haven't changed her tail. It makes the pichu a lot weirder in hindsight.
Having seen so little of the anime I could only suggest Ash's caterpie/butterfree for being so stoic in the face of being disliked by misty and then winning that pink butterfree over and all :'D
Call me basic, but I love Ash's Pikachu, especially in the original series and how much of an ass he was XD
Ash's Charizard. The backstory was sad and hilarious. Plus, the thing is such a jerk to Ash XD #MissingNo
