The mutants of the world who *don't* want to self-deport themselves from the homes and families they were born to and move to Krakoa do need a team of their own. Perhaps there'll be an X-team, in the future, to address the mutants who have chosen not to segregate themselves away from the world, and help them to survive that choice.
Meanwhile, Krakoa can continue to exist, and be relevant, no less able to function as part of the Marvel Earth than Wakanda or Atlantis or Latveria or Madripoor or Monster Island or Sub-Terra or the Savage Land, a 'fantastic' element on a more or less 'normal' Earth. It doesn't *have* to go the way of Genosha or Avalon. It could just be *one* of several options, a new and lasting development to an Earth that's already got plenty of fantastic exotic locales and features.