A.) Something for Ayla.
Um, in preparation for the Ice Age, all the villagers need to collect supplies. Everyone spreads out throughout the prehistoric age. But all the remaining reptites jump them and it's up to you to rescue them! Kino is trapped by the boss!
B.) Maybe a tower in the the Dark Ages underwater, the fallen Zeal. Filled with Zombie Zeals. They're going rise from the ocean and kill the survivors unless you go down and block them off with a magical sealing spell that can only be activated from the throne room. So you must fight your way through everywhere!
C.) Crono's father who abandoned the family when Crono was a boy returns. Unfortunately he has found a weapon of pure evil and is causing havoc everywhere. Follow his path and eventually find him in Truce. Commence epic battle before Leene's Bell.
D.) A rival for Lucca comes in from Porre or Choras or somewhere else saying they have a better robot than Gato and they challenge him to a duel. To get gato ready, 3 supplies are needed. Oil (get from Taban who needs it from an imp in Medina who'll give it up for either $10,000 or defeating his Omnicrone friend), Wrench(Taban lent it to a dancer from the Guardia Festival who'll give it to you if you can beat him in a dance off), and the Steel Glove(obtained by telling Melchior to come with you to the Truce and you must guard him from some powerful robots built by Lucca's rival throughout the cave with a super robot at the end awakening a demon mystic which you fight for a boss battle). Afterward play as Gato in an Arena styled battle with the other robot.
E.) A big race is going down in 2300 AD with more than just Johnny competing! Get in the bike and race against 3 others! The prize is a super powerful arm attatchment for droids.
F.) One grudge holding mystic brings forth the corpse of a warrior in 600 AD... Cyrus! Cyrus now wields a powerful hell bent sword and armor and is causing destruction everywhere. He attacks Porre and it's up to you to stop him before he does anything somebody might regret(HINT HINT piss off Porre, giving Dalton an excuse to portal jump his way in and tell them Guardia sent him).
That's what I've got right now. I might think of better stuff later, dunno.