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I dunno, I think that a lot of my favorite pokes stopped being my favorites after a while, but I'm not really sure about hated to loved. Maybe the zubat line and electabuzz line? Oh definitely mudkip line, I got me an itchin to play through emerald with a swampert one of these days.
I think that the pokemon special manga really changed my opinion on a lot of pokes. Poliwhirl I always loved, and it became my favorite. Swampert, definitely. Drifbloom I've done a complete 180 on since I first saw him. I don't know why.