It simply comes down to, "Do I like this Pokémon and do I want to use it now?" And if I've already used the same Pokémon a number of times, then I ask myself "What other Pokémon do I want to use that I've never used before?"
I'm not really picky when it comes to the Pokémon I use on my team. Sometimes I'd even play the games blindly and use whoever I feel like having on my team at the time. I think this is how I'll play through Pokémon X and Y on my first run through of the games.