It is my belief that the Entity is a Lavoid organism, though an older member of our favorite world-devouring parasite's species. Now, this is mostly wild speculation based on some evidence, but here goes. (Sorry if such has been said before, I've looked around through the forum archives, but there's a lot of ground to cover. ^_^) I also apologize if things seem a bit disjointed. I lost a coin toss with myself and cannot go to sleep until this is posted.
Both Lavos and the Entity have demonstrated similar feats. Both have demonstrated advanced abilities in the manipulation of time and space, such as the creation of gates and the events of the Time Crash. The sudden decline in human evolutionary development after the fall of Lavos suggests that there was some force manipulating human genetics either before the fall, or before Lavos got his hands (or,shell fragments, rather) which may point to the Entity either uplifting humans like Lavos did, only to lose control over them leading to a de-evolution, or the Entity consciously kneecapped humanity because it saw what Lavos might (and did) do with the species.
The reliance on the energy of the world is another point of speculation. It's told and accepted that as Lavos feeds on the energy of the world, the Entity dies. However, the draining of energy is also something Lavos has to deal with, with his civilization-destroying retaliation against Zeal for the ocean palace as per other analysis. The Entity, apparently unable to strike at Lavos directly, instead we can see the Entity helping Crono and company on their Lavos-destroying quest. But, if the Entity is a Lavoid organism, it has another reason to stop Lavos. The affliction of the Entity may not be direct draining, but starvation. Given the guess that the pocket dimension Lavos uses allows it efficient draining of energy from all eras, Lavos may be out-competing the Entity for food, preventing it from gathering energy from the planet.
If the arrival of Lavos is the K-T impact, the arrival of the Entity would likely be along the lines of the Panspermia hypothesis, with its arrival potentially taking place >2 billion years ago. However, (and now we get into REALLY wild speculation) given that Lavos survived a direct nuclear strike from the nations of 1999 AD as well as the kinetic and thermal energy resulting from its own barrage, Lavos may be capable of absorbing large amounts of energy from explosions, impacts, and heat. After all, with its pocket dimension's opening deep inside the planet, Lavos has plenty of access to geothermal energy. The climate of 2300 AD and the use of domes in 1999 AD could suggest a gradual cooling of the planet, which may point to Lavos. If such a feat is possible for the species, the Entity could arrive during the formation of the planet, using the abundant thermal energy of the molten surface both to fulfill its own needs, and set the stage for life.
A >2 billion year existence would give a Lavoid Entity more than enough time to breed, send off its children, and settle down to sustain itself non-destructively with what the planet produces. As demonstrated by Lavos and the Frozen Flame, inciting the evolution of life and manipulating lifeforms is well within the means of a Lavoid organism, perhaps life on the planet was the result of the Entity growing bored. It would explain its ire in Chrono Cross.
But, like I said, wild speculation. Maybe the shocking revelation promised for CTDS will finally end the Entity speculation once and for all. ^_^
