Let's see...
In the Middle Ages, Schala would have never joined Ozzie and the likes. She was older, as well, and powerful. Ozzie and the Mystics wouldn't have exerted control over her. She would have likely left, without harming them too much, if it all, and gone on her own.
Schala, without her mother pushing her around, would probably feel very alone and aimless. She would be torn to pieces by sorrow for, well, everything, and wandered. Oh sure, if a plot needed it, she could find a new calling. But really, I see her living alone, as a hermit of sorts, that maybe could have made her like, a side quest giving type of character or simply a random mysterious mention (the old lady with strange powers who healed people but disappeared from that cave in the lonely woods of whatever, type of thing)... not unlike Belthasar the first time you see him.
And who knows, maybe, like Belthasar's second appearance (kinda), she could have been the one to charge up Marle's pendant so they could get back to Zeal, something like that. Upgrading her to something like Melchior's status. Or any of the Gurus I guess.
Meanwhile, the Mystics still would have gone to war with the humans, that clash seems inevitable, but it also seems it would have taken much longer to build power. They had Magus to rally around, which surely served as a force of unification (I understand Magus was somewhat based on Muhammed the prophet, erm, warlord). Without him, it wouldn't have happened at that juncture.
But then, perhaps without that unifying force, the Mystics would never have unified that way. Sometimes a single person in history can radically change things. Maybe the Mystics would have remained fractured (I'm just assuming they were for the time being) and disorganized. This opens up near infinite possibilities for their progression. We don't know much anything about their society, or lack thereof, from the game, so it's all guesswork.
Which leaves Guardia. Without the war in 600, would they have done better or worse? Again, don't know. The way could have been one of those that forever altered their course from moving toward greatness, to a lesser level of achievement. Think what China could have been had it not destroyed its own navy in the... early 1500s I think.
Or, perhaps the war against the Mystics is what rallied the various human powers, from Porre (for the time being), to Truce to even Choras. Maybe without the war with the Mystics, humanity wouldn't have been ushered into such an era of peace, but the infighting would have continued, and the height achieved by 1000 wouldn't have been so good. Again, not enough information to venture a decent guess.
Back in 12000, I see Janus being a sullen little grudge-holding kid forever. I mean, he was in 600, why not then? In the Lavos timeline, he probably lived out his life unhappily and that was that. (Like, apparently, Schala did? Though I don't know that I buy that.) But in the Crono timeline, when Dalton shows up, I see Janus either being used by him (unlikely unless coerced), which would eventually backfire on Dalton... or Janus confronting and likely immediately killing Dalton. (Recall that Janus was said to be more powerful than Schala.) Unless the Golem Boss was somehow able to defeat Janus. Either way, no one would have been leaving that era.
One consequence: Dalton would never have been thrown to 1000 era and done that stupid-ass Porre militant thing. The other reverberations... Well, presumably, as civilization restarted in 12000, it would have trudged along either way. The small differences echoing from that butterfly effect, so long ago? Yikes, could be nothing, could be everything.
Or, maybe Dalton summoned the Golem Boss, Janus whooped its ass, and Dalton still got sucked into the thing to do that retarded Porre takeover plot line, because it was destined to happen. Since we like fate and dreams and destiny and all that in JRPGs. Who knows.
As for Crono and co... Well... their arc could have remained if they'd learned from old-lady-Schala in 600 that Lavos was a creature of blah-blah-fill-in-some-details. The entity (which I maintain was actually Schala, so figure THAT part of the story out) would have had to send them on a very different path via timegates to get them back to Zeal after visiting 2300 and learning of Lavos's apocalypse... That, once again, can go in near infinite directions. Eventually they'd have to be lead back to Zeal, but how? I dunno, figure it out, entity.
Or they just never did anything and became crazy people warning of an apocalypse in 999 years, which was too coincidental a number if anything else, possibly spawning a small cult that turned into a religion... and in any event, never saved the future.
Or Lucca eventually invented a time machine and they went on their adventure regardless, and still saved the future, but the story arc was lame and Chrono Trigger sales never would have been that great, which reaches into our universe, and this very forum would never have existed because none of us would be compelled to have this discussion.
Hmmm, what else..? That covers everyone, does it not?
