I loved Champion Cynthia too!
Cynthia has pretty good characterization throughout the game because she helps you along your quest and helps you defeat Team Galactic. That's often more than can be said of other Pokémon NPCs.
Plus, her team is amazing! Playing through Pokémon Diamond, Pearl, or Platinum for the first time, new players would probably have heard of rare Pokémon like Spiritomb, Milotic, and Garchomp. But chances are they weren't able to acquire any of these powerful Pokémon before the Pokémon League considering their rarity and strength, and when they show up all at once in the final battle it just shows Cynthia's strength and skill as a trainer!
I think Gamefreak realized this too, since Cynthia makes future appearances in Pokémon Black and White and their sequels.