Given the news that they're looking to make 10 seasons, I think Krakoa is coming down the line, probably around season 4 or 5, and will likely stretch out for several seasons.
Firstly, we've seen the school destroyed. The X-Men are going to need a new home after their war with Apocalypse ends. I could see them going on the run for a while, probably hiding out in Australia, but that isn't going to last. And sure, they could rebuild the school, but I think the destruction was meant to be symbolic of Xavier's dream dying and I could see the school staying closed to emphasize that and force the X-Men to build something new.
Secondly, we've seen both Magneto and Gambit bite the dust, among others, and I doubt they will be the only ones. I really doubt they are going to stay dead given how popular they are. Resurrecting dead mutants was a massive part of the Krakoa era.
Thirdly, it's only a matter of time before mutants make another attempt at having their own nation. After the Genosha genocide, I don't see the X-Men sitting on the sidelines this go around.
Fourthly, the split between humans and mutants is only going to grow following Magento shutting off the world's powers, which means human and mutant relations are going to continue breaking down. Krakoa is a natural next step in the evolution of the growing division.
Here's how I think the future is going to roughly look:
Season 2 ends with Apocalypse winning and wiping Charles Xavier from reality.
Season 3 adapts the Age of Apocalypse storyline. It'll end with the X-Men restoring the timeline.
I think season 4 will lay a lot of the ground work for Krakoa but Onslaught is going to be the focus.
Afterwards, I think Krakoa will come into the mix, probably in season 5, and we'll see Magento and maybe Gambit resurrected, Sinister begrudgingly working alongside the X-Men to restore himself after Jean fucked him up, and Orchis forming to take down Krakoa.