I was thinking of the Pokeballs that we have in game at the moment. Yeah the Master Ball is one per game (more if you're lucky). What if there was an "X ball" based off the type of your lead pokemon and the target you're trying to catch? You have a water Pokemon in the lead while trying to catch a Fire Pokemon? Great the catch rate goes up a lot.
Or a change to the level ball? How about as your party gets higher in average level, the catch rate goes up?