It's funny, because I'm actually having to think about this question, since I usually just make the decision on whether I like a Pokemon or not quite quickly and never give it another thought XD
Well, firstly I'd say it is looks. I tend to go for Pokemon based on animals over those that are mineral/tech/human based or whatever. I also tend towards those based on animals I like, such as Foxes, Birds or Prey, Otters, Rodents, Cats etc. On the flip side I tend to automatically dislike Pokemon based on animals I dislike, such as monkeys (Don't hate me).
Because the game limits who's available, I also sometimes develop a liking for a certain Pokemon by accident. If I've just played through a whole game with something, odds are I'm going to have grow attached to the little bugger. Also, sometimes just by giving a Pokemon a chance I start liking them. Weavile is my obvious example of this. I really didn't like Weavile, just something about him bugged me. But then Linkachu and I played some Battle Factory on WiFi. Weavile was pretty much the only usable Pokemon I had to choose from, so I used him. I've never looked back since and a Weavile has a permeant spot on my completive team ♥
I've never based my likes or dislikes on usability in battle, but that's possibly because I only got into competitive battling a couple of years ago - therefore I already had opinions on most Pokemon beforehand.
Shallow, but if a Pokemon has an annoying back sprite I seriously consider whether to use it in game :V
Finally, Type can sometimes sway my opinion. I have always seemed to lean towards Dragons, Fire, Ice and Dark Types. There aren't many Water, Poison or Grass types that I like either. Although Sceptile and Vaporeon are two of my favourite Pokemon~