Ayla, the primitive cavewoman from 65,000,000 B.C., through a feat of great irony, is quite similar to Moses, from the Old Testament. Moses was the character who received the Ten Commandments from God atop Mt. Sinai and led the Israelites to freedom from their slavery in Egypt. Her parallel is quite strong, and was probably intentional.
Similar to Moses being called to Mt. Sinai through visions and the beckoning of God to receive the Ten Commandments (which contained the will of God), Ayla has a dream that Crono and his party are wounded atop Mystic Mountain. She thus climbs the mountain, and retrieves Crono (parallel to Jesus, the son of God). While the retrieval is of a godly being and not two godly tablets, there is a curious likeness here in the retrieval of a godly item from atop a mountain through a vision.
Just as Moses led the imprisoned and enslaved Israelites to freedom from the tyranny of Ramses II of Egypt, Ayla leads her imprisoned fellow humans to freedom after they are kidnapped by Azala (similar to Ramses II). Here we have the Exodus.
Moses is said to have entered the "burning bush", where he was given the duty by God to confront Ramses II and demand that his people, the Israelites, be freed. This, of course, is represented by Ayla (Moses) entering the "burning forest" of the Laruba tribe, and there makes the vow that she will storm Azala's (Ramses II) Tyrano Lair and free her people (the Israelites).
It has been brought to my attention by Dark Magus (firstname.lastname@example.org) that there is a strong similarity between the Laruba Tribe and the Israelites of the desert during the time of Moses. These Israelites lived far from society in the desert (as the Laruba lived far away from society in the forest), and always blamed Moses's intervention and attempts to free his people for their misfortune (as the Laruba always blame the misfortunes of the humans brought upon them by the Reptites (Egyptians) on Ayla's constant intervention by fighting the Reptites. As did the Laruba Tribe, the Israelites of the desert did not want to get involved with the struggle of freeing the enslaved Israelites (humans).
The Book of Moses is very old in comparison to other parts of the Bible, just as Ayla and her story are very ancient in comparison to the other stories and characters of Chrono Trigger.
It has been brought to my attention by Sephiroth that the name Ayla was also the name of a cavewoman in an older movie about prehistoric life entitled "Clan of the Cave Bear". It is most likely that this is the character Square named Ayla of Chrono Trigger after.