I normally think on the personality of my character, because that's usually how people decide who they want to have on their team to make it champion. however, I also think about what the pokémon are for, and the age of the character. Everything is about to putting yourself in your character's shoes.
For example, if I have a very sweet little girl who wants to become a coordinator, I forget everything I know about pokémon, because she is inexperienced. I take a look at all the pokémon, and pick the six that look the cutest, or have nice, pastel colors in them, then I can even go as far as to ask a little girl who she would like best, and whatever she chooses is what I use.
On the other hand, if I have a thirteen year old guy that loves to battle, I pick the ones that are believed to be, or look tough, but I may add a small, commonly weak pokémon that could teach the kid that winning is not everything.
All in all, it would depend on what I want to happen in the story.
I hope I helped =D Good luck!