For me it was Fake Groudon, Luxray Tribe, and Primal Dialga. And after the main story it was the Guild and Palkia that gave me trouble for a while. Darkrai was easy for me, it wasn't too much to beat all his minions, just make him incapable of action and fight his minions. The hardest part about Darkrai himself is how he kept usin' Double Team over and over and causes you to never land a hit.
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