Firstly, I dislike Emolga. Almost every time when I'm Audino-hunting, Emolga pops up from the shaking grass. Come on, all I ever wanted was just an Audino, the higher percentage of shaking grass dwellers? :/
I also slightly dislike Basculin. It tends to be about the only pokemon that appears when I'm surfing or looking for a specific pokemon. >< Put that reason aside and it's alright.
Okay, dislike based on looks? Let me see: Patrat (those eyes and that tail!). Female Unfezant. Woobat & Swoobat. Timburr & family. Trubbish & Garbodor. Gothitelle. Klink & family (they're just a bunch of gears..). Amoonguss. Stunfisk.