I never thought I'd be saying this but, Pikachu.
I always had something against Pikachu, I just never liked the guy and overexposure played a part in that. ThoughTravelling around with Pikachu in Yellow is a feeling I'll never forget. I could genuinely feel myself getting attached to my mouse companion. Whenever he fainted I would rush straight to the Pokemon centre, I refused to use the bike or deposit the little guy in the PC so I could walk with him and seeing the little guy jump side to side being distressed over you being seperated from him by a cliff is a touching little detail.
I would bring him to battles as much as possible. I let him take on Lt. Surge and deliver the final blow to Brock's Onix. Despite the odds not being in his favour.
To top it all, whenever he fainted in battle and I heard that cry, I felt bad for letting him down.
Pokemon Yellow gave me a whole new appreciation for the little rodent.