Reports are hitting that Marvel is putting some real commitment to X-Men 97, with season 3 and 4 in production. Reportedly, season 3 is nearly complete for scripts, while season 4 is in the conceptual stage.
I suspect season 3 might (following trends seen in season 1 and hinted at in season 2) end up a loose adaption of Onslaught and Hunt for Xavier (with maybe a dash of the “Children of the Atom” arc in there as well). It feels like a natural point from seasons 1 and 2, and by the time the season would have been in production in the 90s (circa 98 for airing in 99), Onslaught would have been a recent “big thing” in the comics.
Not sure where season 4 might go, but I think it might be nice for more stand alone episodes and maybe “micro arcs” instead of the larger arcs seen in season 1 and hinted in season 2. Might be fun for a 5 part run dealing with some space shenanigans like the Phalanx invasion of the Shi’ar Empire.