There's a huuuuge difference between "Villains" and "Antagonists". I think the best stories told are those that feature Antagonists who are not Villains...
Phoenix and White Queen have often been portrayed as Antagonists to each other. Wolverine and Cyclops. Cable and Bishop. Avengers v X-Men. etc etc etc
In that way, Polaris gaining a well-written antagonist relationship with a fellow hero / X-colleague, it could be great for the character, especially as she then develops her "side" so to speak... colleagues (X-Men) who have her back.
Yeah, I still have faith she'll end up somewhere. I just hope the rumor of a final X-book is true, and she's on the premiere issue cover. Because #1 cover spots boost IPs like crazy.