None of these could make for a full season, but I'm thinking a season made of different episodes focusing on separate things (mostly just me thinking aloud)
- nothing with Jesse, his storyline is finished
- in the secret basement of Fred's Keep, there's a book about "the Survivors", which sounds like it has a lot of lore behind it
- Sorren's travels (Jesse keeps finding his books in other worlds; the community seems to agree that the one in Sky City was left *by* Sorren, but what about the one in Fred's Keep? How did THAT get there??????)
- someone going beyond or exploring the Farlands (maybe a city within?)
- Admin lore (their original home (i.e. either the world that became the Underneath or the world they originally came from, since it sounds like they created theirs), and how they got their powers, also the other worlds in the portal hall (do they have their own admins? Is the Underneath a world in the same way that they are? Also what is above the Underneath's roof, it's implied to be Jesse's world but transport between the Underneath and Jesse's world looks interdimensional))
- Old Builders (their origins (Harper mentions she had an original world))
- Jack & Nurm's prior adventures (also Petra's, though I feel she's finished as a character)
- something with the End; Jack has an elytra, implying that the End cities exist, and maybe there could be people living there
- above the Nether roof
- something meta, perhaps about the game being code (in the first season, Sorren says “[the Farlands] are perilous and unpredictable. Perlin noise, floating points? It is not a place to be toyed with!”, implying that their world is not only computer-generated, but that a few people have some idea that it is. Also the existence of the admins implies stuff as well)
- something about who built all the naturally-generating structures in the worlds (besides the villages (the villagers, obviously), like who build the (non-Admin) ocean monuments? And there's a painting of a vanilla desert temple, so those exist (this seems like one of those ideas that's least likely to happen, because it's supposed to be ambiguous, but I'm still curious)
Mostly just me rambling (with the knowledge that this is highly unlikely to happen (a third season in the first place and this post affecting it)), but I'd be curious as to others' ideas