30% design
10% battle potential
60% personal compatibility
By battle potential, I don't necessarily mean whether or not it's the best or higher tier, but whether you can actually do something with it.
By personal compatibility, I mean whether or not I can relate with the pokemon. I'll admit some of my favorite pokemon don't have the best designs, yet there's something about them that click with me. Take Shroomish. We already had a mushroom pokemon, nothing very exceptional about it. Yet there's something about its colors, lack of arms, stubby feet, and that face that makes me like it so very much! ^_^
A majority of my favorite pokemon are the unevolved, smaller stages. Lots of them happen to be green.