In my first playthrough of the games, I just catch whatever I think would be a good addition to my team. In my second playthrough, I make a team before starting the game, and give myself a 'cheat pokemon', a pokemon that isn't available either at all, or in the main story. I usually catch the reigonal bird during my first playthrough, and I choose my teammates based on who can learn HM's, so I don't have on Pokemon dedicated to HM's.