Best animated incarnation of Jean Grey hands down(WatX version too, but barely shown, though her original 5 flashback telekinetic, City bus showdown with Magneto was pretty amazing)
Like others have said, Season 3 is where it really comes into its own.
And for me, it's kind of how things can be different, but not better or worse, just different. Like NES Zelda 1 vs. Zelda II. I loved TAS's verbose and dramatic Apocalypse...but there was also something very badass about Evo's version, when both the X-men, Magneto and the brotherhood all try to attack him, Egyptian-esque music in the background, slo-mo pans, etc, and unfazed Apocalypse says nothing, barely turns, the music goes silent, he clenches his fist, and power wave knocks everyone out...the music resumes and he floats on about his business.
I also liked that evo had actual roster changes...on both sides, and not just the usual one-off cameos most shows would do.