Sabrina is the hardest for me; none of the starters are all that good against her, and the gastly line is weak to psychic attacks because of their secondary poison type. There are no other ghosts, and you can't have a dark type until after you've defeated the E4 and gotten the national dex. All in all, it is simply hard to land super effective hits on her pokemon. And, IIRC, there is a significant level jump beetween her and Koga/Erika (I say Erika because alot of people beat Sabrina and then Koga) So your pokemon, aside from being normal damage at best, are at lower level.
That's how it is with my game, at least.
pikapras
EDIT: I know that you can have a dark move, but you can't have type advantage.