First of all Til the End of Time really does need a remaster. Hands down one of my favorite RPG's of all time. However what doesn't make sense about the timeline? What is years and years of time in the "Eternal Sphere" could be much less in 4D. I like to think of the Eternal Sphere as a procedural generated universe. With alternate universes. I think this would make sense when Luther says he had a problem trying to eliminate flawed code with the Executioners and then tries to reset the entire Eternal Sphere. It all seems sensible in my mind. He created the universe with a base parameter and let it grew and tinkered when necessary. He just tinkered too late and the "Data" learned too much. Just my thoughts. I don't know if that answers anything for you though.

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There is surely some plot holes though. Reminds me of the Alien moves from Ridley Scott, but they're still good movies nonetheless.

Luther was the creator of the Eternal Sphere wasn't he and the timelines in there are like after every few hundred years or so

Yeah I understand the timelines are quite some time between each other but the Eternal Sphere is just a simulation so the time itself may not really be that much time in their perspective. Then again if you take the fact in reality the Earth is billions of years old I don't know why a person would create a universe with so little and wait that time for it to blossom into what it was. I don't really know. However, take the newest Star Ocean game as well. They put it before Til the end of Time. Probably because anything past the "End" of the Eternal Sphere would make people uneasy or skeptical. Just a thought.

well i honestly think they didn't create the Sphere at all just opened a gateway to another world

Never thought of it like that. However how come Luther was able to destroy the Universe then? You see the galaxies disintegrate at the end. They are in fact two different worlds. Luther is in "4D" and everyone else "3D".

he didn't destroy it as the ending clearly shows