Scroll to the bottom if you just want the short version of this.
So we know that the Chrono Trigger team may have made some errors during the first game (Dalton and the fall of Guardia). We also know that they were fighting against an expected outcome and doing their best to defy it, which is a theme also dealt with in Chrono Cross (Dinopolis and the Dragon elements vs. humanity).
With these in mind, let's look at a few things that make Chrono Trigger lead to Chrono Cross (since, obviously, if Lavos is never defeated,
One is the time egg(s). These are fairly rare, pretty powerful, and capable of going to key areas in space and time. However, what if the first one was misused? What if only one was needed, and all of Chrono Cross could have been avoided?
Let's look at the first use: saving Crono. What makes his death an important period in time? What makes Crono worthy of being saved? Many people die in the course of the game, either directly or indirectly (lots of people in the future). Without Crono, Lavos probably would have killed everyone in the Ocean Palace. Whoever remains probably wouldn't be able to defeat Lavos. Crono is needed to take the brunt of the attack to save the others.
But after that? The game creators seem to hint that Crono dies. While there is some evidence that this isn't true, part of it may be wishful thinking. Lucca most likely died, so why not her friends? Robo makes the ultimate sacrifice as well, so the death of characters isn't too important, just what they do with their lives. Crono's life seems to have been focused around saving his friends, and afterwards, because of the time egg, he's given some extra time. There's no arguing that Crono is needed for defeating Lavos, but he's not needed in the actual battle (you are able to defeat Lavos without him, whether he's dead or you just choose not to bring him). What purpose does Crono have after his first death that isn't filled out by someone else? His sacrifice is important enough to return to, but is he the one that needed to be saved?
While in the short term, both the player and Crono's friends seem to regard Crono's life as important, but in the long term, Magus may have unknowingly hinted at another possibility: Schala.
Schala's future is what causes Chrono Cross. Schala, unlike Crono, has certain advantages in the timeline of the world. Her fusing with Lavos is much more meaningful than Crono's marriage in the long term (unless Chrono Trigger 3 comes along and proves me wrong). As much as we may love Crono, Schala may have been the better choice.
But so what? We're given the tools to save Crono. What else could have happened?
There's a few options here. The first is that, unlike Crono, Schala doesn't die. If, rather than traveling to the moment Crono dies, one were to travel to the moment Schala sends the group + Magus to the past, one could simply bring Schala back and avert the whole mess. No clone needed (in this version). Schala probably would have made as good a companion as Crono, and is also vastly more powerful, and would have helped out greatly in the battle against Lavos. Lose one person, gain another, and avert a horrible, dimension and time eating monster. Sounds fair enough.
But what if the gurus are correct, and that, whether or not someone dies, a clone is needed to take someone's place? While Norstein Bekkler may not have had a clone on hand, someone else eventually would: Lucca. What if Kid's purpose was only to replace Schala in that moment of time. What if, on some level, Lucca realized that? Is that perhaps why she began to make a time egg herself? Did she realize the group's error and try to have a back-up, in case Kid would need to make the ultimate sacrifice?
Condensed version and conclusion: Perhaps the player was not meant to use the time egg to save Crono. There was nothing in particular that was remarkable about Crono aside from his desire to protect the people he cared about, and while this is a rare trait in people, the group seemed filled with like-minded individuals. Had the group saved Schala, either by using the time egg immediately and not used a clone, or waited and used baby (or later had a grown) Kid to take her place, the events of Chrono Cross would not have needed to happen.
While this may sound sad, there's an upside: the series is about defying fate. Defying the expected. While in traditional heroic tragedies, people sacrifice themselves for others, as Crono did and what some may have wished Kid to do, the protagonists instead make a selfish decision to fight for those they care about, even if it means dooming others. It's human nature. Schala was just as heroic as Crono (if not more so) in the end, saving people she barely knew rather than saving herself, yet because he was a friend, Marle and the party save Crono. However, if the actions of Serge and his party really did reverse a lot of the "bad stuff," perhaps this is justified in the long run. Despite the suffering caused by this selfishness, is was only temporary.