How about this? Like, different things you do determine how your game plays out.
For example, there are some optional sidequests that determine whether you fight rival on route whatever or right out the fifth gym. Or even determines your champion out of a possible 3 people.
Or even the sidequests could change, like if you chooseto wait to rescue a clefairy from ruffians kicking its ass, come back later to find out the clefairy was rescued by another trainer, only to see them later on to fight you using that clefairy (now a clefable) --- Xerneas is Psychic/Rock, Yveltal Dark/Flying (speculation)