IDK, I thought Onslaught was a good mission choice for Phoenix/Jean Grey, seeing how he's a psionically powered viilain. I mean, he was literally "created' when Xavier's vast mental powers forcibly removed and then merged with all of Magneto's dark thoughts, feelings, & emotions. Jean also played a HUGE part in the storyline, which was a massive crossover event, that led directly into the controversial Heroes Reborn. I know it was a mixed bag quality wise, even back then, but there were some key moments for me. Like when Hulk came to Jean in the midst of their last major battle against Onslaught in NYC, and Bruce asked her to sever the control he then had over his Hulk persona. This was so Hulk could access his maximum rage & strength in an attempt to defeat the villain, who also had child hostage Franklin Richards in his clutches. That to me, was a wicked cool character moment between two heroes that don't normally get to interact. And actually what he asked her to do, what she did, was a pretty big deal I think.
So far for X-villains, we have Magneto(of couse) x 2, Mystique, Sabretooth, Juggernaut, & now Onslaught. I think we X-fans are doing OK, lol. But you're right, there are still so many others that could yet be used. The aforementioned Apocalypse(who I'm almost positive we'll see at some point), Sinister, the Brotherhood, the Hellfire Club(Shaw & Selene are just too sick & vicious), the list just goes on & on. Hey, how about the Shadow King?! I've always felt like he was a real malevolent & scary badass, we could fight him on the Astral Plane!