He wanted a starter Pokemon from Hoenn like Torchic because they were "special", or a Pikachu like Ash Ketchum, who he seemed to have heard good things about. At the beginning of the episode, he didn't really understand the point in having Pokemon other than for protection. He didn't want the hassle of raising them and was quite spoiled and selfish, making lots of demands for evolved and rare Pokemon like Raichu.
However, while accompanying Professor Oak and the others during the episode trying to recapture the escaped baby Bulbasaur, Charmander, and Squirtle, he begins to learn a lot about the feelings of Pokemon and grows to understand them. Gilbert eventually chose the Bulbasaur he'd helped save from a group of Primeape after he was impressed by the strength of Ash's Bulbasaur at driving them back with a SolarBeam.