>>29052802I posted once before about how I think Ash could be moving all his pokemon to Cousin Oak's in Alola where his interactions with them could be more flexible. Since Ash-Greninja is actually in Sun and Moon, this seems like a substantial hint that it won't totally be left behind. I can see Ash keeping Greninja around for training but not using it on his Alola team, or at least until the final trial or something.
Also since Ash went and promised Greninja that they'd become strong together, then renewed that vow the writers sort of prevented themselves from getting rid of the frog in the usual way without looking like total asses.