>>529644514
It feels like they hinted very early on that knuckles would guard the chaos emeralds, along with the master emerald, but never committed to it.
It'd be the perfect excuse to have him still running around with the main cast, and logically makes sense since the master emerald is supposed to neutralize the chaos emeralds anyways.
I don't think they'll do it at this point, but its the best idea I can come up with.