Time Periods I was thinking of using were 1999 AD, 2325 AD, 11975 BC, 7600 BC, 1 AD, 1025 AD, and the end of time (at least). Villains would have been King Zeal who's goal would be to rebuild Zeal but would be unwittingly carrying out Lavos will, and therefore cannot be allowed to succeed. Dalton would be Zeal's deputy but also with an agenda of his own.
There's some cool ideas around Asteria and the 7600BC era. Did you happen to play Crimson Echoes? You may like what they did with King Zeal in that game. 
I Watched the playthrough on youtube, I do have the game though but so far I'm near the beginning of the game having only gotten to when the party first meets frog again and first visit the Medina continent with the vanguard.
Regarding Asteria I actually happened to be inspired to write about my ideas about her and 7600 BC because just yesterday I happened to stumble on the net on believe it or not the movie trailers for the new sci-fi/dystopian film Mortal Engines. What seems to be The plot for that film just happened to have a similar trajectory as my Ideas for Asteria and the 7600 BC era. Although Mortal Engines has obvious differences from Chrono Trigger though.
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