I'm spotting a possible weakness in the plot: the Dragon Tooth doesn't seem to be integral to the plot of the game. Its only notable usage is to make traveling from the past to Chronopolis possible without Time Eggs or pre-existent Gates, which in fact only applies to 1 AD and the trip to the 12000 BC Ocean Palace before the Frozen Flame nightmares. It's used in so few instances that we might as well remove these instances. We could declare that the Entity creates a permanent Gate in 1 AD after what Marle experiences; as for 12000 BC, we could simply have another Time Egg breaking.
I'm not saying we should remove the Dragon Tooth itself though. It just needs a more important function... Perhaps it could be revealed in Singing Mountain that the "Dragon Tooth" is not an artifact, but actually a Reptite shamaness? The party, dumbfounded, would still try to bring her to Belthasar. However, King Zeal would appear in the Lavos crater as in the current plot. In addition to the party members, the Dragon Tooth would also be warped through time along with a male Reptite, to some random year BC.
This new plot point can perhaps make the Reptite timeline more credible. It feels curious that the humans could survive for 65 million years against the Reptites in a warm Ice Age. So, what if King Zeal's spell doesn't change history, but instead, the two Reptites do? The Dragon Tooth and the male Reptite would reproduce and create a population in whatever BC which would compete with humanity and changes history. Marle would arrive in 1 AD to witness the end of humanity; then the alternate 1002 A.D. and 2001 A.D. would be like it is in the current plot.
When Crono, Glenn, and Magus return to Prehistory with Sorin, the latter would be the one to revert the alteration: he would heroically jump in the Dragon Tooth's portal, would arrive in whatever BC to kill the Reptite couple, and would presumably be stuck there for the rest of his life. "Whatever" BC is never explored directly, but the party could discover Sorin's age-old corpse in a cave in a future era or something.
I believe this new stuff connects the King Zeal, Sorin, and Reptite story arcs better than currently. This may change Chapter 16 (Stop the Porre Lab) a bit though, and Dalton still has to be integrated somewhere.
Thoughts? Is it credible to have two Reptites "recreate" a Reptite population? We could have more than one male and one female warped, but I don't want to go overboard.
EDIT: "Whatever" BC could perhaps be 3,000,000 BC, meaning that the new Reptite population would be affected by the Frozen Flame taint like the humans.