Once upon a time there was a great evil that threatened to destroy the world.
Somebody's trying to awaken it!
You try to stop them, you defeat them but they're able to awaken it anyway, you stop it.
Okay, why does this being want to destroy the world? What does it/he/she/xe gain from doing this? That's never explained. Doesn't matter if it's a human or some kind of supernatural entity, I'd like there to be a reason. I'm not sure if a lot of games still do this, but it's boring when the enemy is just "evil" for the sake of it.
Another thing is when a villain has awesome powers that they never use in combat, only in cut scenes or backstories. I know the Zelda series is guilty of this a lot. After you beat them it's just like "Why didn't you do that thing you did earlier?" Usually it's a power that would be very hard to counter or avoid, too, which could make for more challenging fights.