Pretty sure Gyms will be back, for the simple reason of Sinnoh remakes. I guess they can expand how they work in other mechanics, but I doubt they will bother will that since I suspect they will try something new for Gen 9. The only obvious replacement I can see is introducing Tournaments instead of Gyms and Trials. That would allow for some RNG based progression.
That would be really clever, actually, and it would give some uniqueness to gym leaders' aces.(or give each gym leader a totem)