They already had that plot device. The Phoenix magically re-mutated (some of?) the people No More Mutants 'normalised' and has spurred the creation of new mutants. There's a handful of the newbies in the JG (Shark Girl, Eyeboy, Sprite) ,Xavier (Time Girl, Healer Boy, Golden Balls) schools. The Hellfire school too (Lobster guy and Snot probably counted, Android guy probably didn't, and I'm not sure about Infestation). I assume perhaps the Pan-Asian/Latverian/Capt.Brit/etc. schools probably have a couple between them too.Mutants have been on the brink of extinction for awhile, so unless they bred like rabbits the past few years, it's hard to think of a plot device that doesn't involve time-traveling to replenish the mutant numbers.
And then BOTA kind of did the time travel thing too.