Apparantly, you haven't fought Alder's PWT team, which is said to be harder than his usual team. As for Cynthia, her Garchomp is still a pain unless you wear it down (while hoping Dragon Rush's not-so-good accuracy is actived more often. The reason why they replaced her Milotic with Glaceon is because of Wallace, who uses it as his signature Pokemon. If you're talking about their levels in BW2 compared to BW1, I think GF wants the player to face them earlier, after beating Iris, to unlock some of the post-story's features (i.e. Black Tower/White Hollow).