I too remember my first battle with her in Pearl, way back in 2007, haha. Battles with her are always something to remember, I can assure you. My most recent one (my Ground Monotype back in the fall) she did put up a good fight, bringing me to only two Pokémon, but still winning without any items.
And her character was quite good too, you see her quite a bit in the story as she talks about different aspects of the region, including being interested in myths. (Also, in Platinum your rival mistakes her for your sister, which was funny.) It was also great seeing her in the Unova games, that was fun battling her.
So yes, I would say Cynthia is my favorite Champion. But I do find it disappointing that she not only leaves you to cure a bunch of Psyduck that are suffering chronic headaches and not feeling inclined to move at all (don't you think it's kind of cruel to leave them suffering there like that when she could be curing them herself?), but just tags along with you in the Distortion World but ultimately does nothing productive.