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Cynthia, she has the best team out of them all and is the hardest to beat imo. Iris in B2W2 is pretty good as well though, particularly on Challenge Mode as her team all use held items. I just wish all Champions did something like that to add to the challenge.
No one mentions N (Black and White). I love the dude. He was the most difficult champion battle for me. Shoot, I even played platinum and I beat Cynthia on either my first or second try.
Alder. Blue, Lance, Cynthia and everyone else are strong, but Alder is the first champion who shows a care for both Pokémon and other challengers outside of league and he always seemed pretty wise.