I don't like how it rendered the whole of Chrono Trigger pointless. I haven't actually played the game, so I'll quote from TV Tropes.
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Originally Posted by Shoot the Shaggy Dog page
Remember the super mega happy ending you got with Chrono and Marle hooking up and pretty much everyone except Magus going home to their happy new worlds? PSYCHE! They all die! Oh, and your actions caused millions of people to never be born and get flung into non-existance and curse your existence. Time Travel is in fact a horrible thing that causes worse things to happen. The world in the future collapses thanks to the technology created by Lucca. And Schala merged with Lavos to become an even more powerful, unkillable being that Chrono and his friends cannot defeat. And Dalton, a minor mini-Boss that defeated himself, remembers Chrono and his friends, conviently winds up in their time period, and turns a tiny little town into a world-conquering army so he can murder everyone in Guardia and burn it to the ground. Oh, but Magus lives. He just may or may not be a different character in Chrono Cross. Depending on the Ret Con that day. And he can't save his sister at all, so she rejects him. Aren't you glad you went back in time to save the future?
* Both ports of Trigger released since Cross also added extra cutscenes to further emphasize this fact: The Fall of Guardia did not exist in the SNES version, so the game never ended with "Unexplainable army kills everyone in Guardia including our heroes." The Dream Devourer fight in the DS version was also new and pretty much exists for you to fight, win, and then be told you can't win and get sent back to the past...thus Chrono and his friends cannot stop the horrible events in the future from happening let alone their own horrible demises.
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From what I've heard about Chrono Cross, that's accurate. I don't think
Frog and Ayla die, though. They're dead by 1000AD since they went back to their own times, but I don't think there's any indication they didn't live happily ever after. But like I said, I haven't played it.