Humans overall
Posthumans
Sentinels/Nimrod
Xeno-type groups
Orchi
Other mutants
Alien civilizations
Something else
The writers getting bored with the villains all somehow chilling and not disturbing the peace.
I’d say sooner or later there will be someone who can either subvert the Protocols or worse, burn specific mutants out of the backups
Outside of aliens and other mutants, all the other threats come from humanity, so they continue to be the biggest enemies of mutants.
The writers, who will inevitably feel the need to tear it all down, so that mutants can go back to their hunted status quo, will be the biggest threat to Krakoa.