Hmm, everyone keeps going on about their favorite Pokemon in this thread. Of course my first pick would be Takeshi Shudo’s version of Mewtwo, for such an excellent characterization of him in the first movie and Mewtwo Returns, but I guess that’s not what most people meant.
My top pick for my party back in the day would’ve been Lugia. I loved the design as a kid and was thrilled to finally catch him in Silver. The fact that he was a Psychic/Flying type made for a deadly combo and he made for an excellent trump card against both the AI and friends (that is until I faced Red’s Demon God Pikachu).