SPOILERS
X-men '97 covered a lot of stuff from the comics - The Trial of Magneto, Inferno, Lifedeath, Fall of the Mutants, Operation Zero Tolerance, Fatal Attractions and E is for Extinction, and probably a few I'm missing - even touching (a little) on the Krakoa era.
Season 2 looks to be setting up an exploration of Apocalypse's origin, and some variation of The Adventures of Cyclops and Pheonix.
That apart, what story-arcs and plot-points from the comics (or elsewhere) would you like them to explore in the next season, or beyond?
I kinda want an adaptation of Giant Size X-men # 1, which hasn't really been done before. I suppose it can be reworked as a 'present-day' story but I'd prefer it to be a flashback which shows how the TAS line-up came together. It'd be the best way to set up Krakoa for a potential adaptation of that story down the line...
Since they've shown themselves to not be averse to post-90's material, maybe they can touch on Origins? I think Wolverine is due a meatier role in Season 2, and with the fallout of him losing the adamantium and rediscovering his bone claws, it might not be the worst idea to explore his early life and maybe introduce the likes of Rose and 'Dog' Logan.
God Loves, Man Kills is another story-arc I'd really love to see done in animation. Reverend Stryker cameod in Season 1...maybe they were foreshadowing this?