A tie between Yellow and Ruby/Sapphire. Absolutely loved the Elite Four in the Yellow arc, and the whole mystery on the whereabouts of Red kept me completely engrossed in it. Yellow also developed nicely as a character. The epic battle with Lance was terrific, and Blaine and Mewtwo were a nice touch.
Ruby/Sapphire was completely interesting, like Around the World in 80 Days. It kept a nice mix of the conflicts between Ruby and Sapphire in correlation with Magma and Aqua. I also loved that Magma Admin (who I forgot her name...) and she was quite the character with her own past revolving around contests. The ending was nicely done, fused with the legendaries and inevitable deaths.