Single Status Update
It's clear that Classic Knuckles really doesn't want anything to do with Sonic unless he absolutely needs to, so other Classic games from here on could very well sub in Mighty for him, so the setting doesn't always have to return to the Master Emerald or Angel Island to justify Knuckles.
Ray's harder to justify over Tails though, since Tails has no animosity at all. Wonder how they'd go about subbing Ray in for that, unless they just go with the four as a set.
I think Ray's connection to Mighty, and now Team Sonic as a whole, is enough to justify him coming back to help in later adventures. But they could just as easily say he, or any of the others, might not be available for a game. They're all Sonic's friends, but that doesn't mean they're obligated to spend all their time with him.