Back.
So, in the last post, I outlined some of the history of Lavos' race, which needs some sort of name. When the Lavoid civilization first got the idea to groom life to join them, his was a trusted and revered name, and he was placed in charge of this effort. He traveled to a lifeless planet and appropriated its resources to create life. For the first few million years, it went well. But that world's race had no hive mind and no innate sensitivity to the currents of time. Thus, the hedonistic nature prevailed within them, and just when it seemed like they were ready to become an Elder race themselves, a cataclysmic war nearly destroyed them and rendered their planet a graveyard. Lavos was distraught at this, needless to say; the stewardship of that world was his, and he felt like he'd let them down. Not only that, he began to question his own ideals. Asking questions of the universe, he found only greed and hatred to answer them. Eventually, he grew to loathe his fatherly instinct. It wasn't much of a step from there to universal hatred.
The Lavoids, meanwhile, were pursuing a completely different goal. A few billion years into the universe's life cycle, they knew that the paradise of the universe's initial time compression, which to them is a paradise of all-encompassing knowledge across all timelines, was fading from them. Having learned the powers of magic, they could survive in the End of Time. However, most life doesn't have this power, and will not retain its own will in such an environment, instead being absorbed into the timestream. There, all that exists is Zurvan; whoever controls the power of magic unopposed will control the universe's outcome if they exist in such an environment. However, the End of Time is such that only one can control this power. If two or more are present that wish to control it, a battle will ensue until one soul annihilates the other completely. The Lavoids had planned to create a paradise in the End of Time using their magic. It would have worked; their minds are capable of functioning as one. However, when Lavos' pain and anger began to seep into the hive mind, the Lavoids were no longer as one; the resultant chaos of a battle in the End of Time could end up destroying the universe.
I think this reworking could solve a lot of plot issues. The Chrono Trigger operates off of the power of Zurvan; it is humankind's tool for channeling it, allowing one to resurrect a possibility that no longer exists. They did it to resurrect Crono, and Serge does it to access the Tesseract. It could also explain why the team loses their power; being exposed to a bunch of angry souls in the chaos of temporal limbo could do that to you. The Chrono Break would still be developed in the lab at Calasperan; basically, nothing from the existing story would change up until Scenario 11, when we'd have to give a different situation for the Frozen Flame. The ending battle would be largely the same, save that now we know exactly what happened to Gaspar; cast astray on the winds of time, he ended up at the End of Time, and effectively became a God due to his magic. However, his wish was not one of paradise or conquest, but simply of preservation for his species and those he loved. In order to utilize the power of the End of Time, one would have to kill Gaspar. With his current status, the only way to do that would be through the Chrono Break; thus, the Sorin storyline can stay largely the same. Part of Sorin's soul could be preserved in the Chrono Break, thus enabling him to lend a hand in the final battle.
As for the El Nido scenario, it's still one of the keys to Lavos' plan to control the End of Time, because it has the only resource that can ensure Sorin's survival, and thus the complete maturation of the Chrono Break. It, like the Chrono Trigger, takes the form of an egg, though its markings and general appearance are substantially different. That resource would most likely be Elements.
The ruined world would also be affected by this new scheme, but we can easily keep it in by saying that the dreamworld is a result of Gaia attempting to keep Earth from vanishing into the timestream; the ruined planet is a result of its compromised state. This will also allow us to be even more extravagant with the scenario by incorporating the near-complete death of the universe.
There's still a bit that needs to be fleshed out, but IMO it's more than what we had to go on before. Plus, it solves the problem of the scheme being too much like Advent Children.