I have 3 ideas which are very or loosely tied together, they're more like theories, but I think they answer some questions. My theories are somewhat fact and somewhat "what if", so I'll point out the fact and presumptions sometimes for clarification. I had decided to post these ideas before I read
http://www.chronocompendium.com/Forums/index.php/topic,5571.0.html and I decided to not only include my ideas but direct my theories at that topic. My post can be read without having to read that other topic, but I think that reading or at least breezing through the other one would be helpful to understand why I make the points and arguments I do. I thought about posting this as a simply reply to that topic, but the scope of my post doesn't stay on topic. I would be introducing new ideas and questions to a topic that's having an interesting enough time trying to figure out answers to its own questions.
My first point is that the Frozen Flame was used to keep tabs on the upper world (though that wouldn't be its only purpose). Lavos showed up to destroy Zeal, possibly showed up in 1999 to stop mankind which could have reached a technological level that could threaten Lavos. If we believe that Lavos wanted to improve the DNA of humans in order to find desirable DNA characteristics to add to its own (kind of like the Borg from Star Trek) then it would have to be aware of the good and the bad. It makes a lot more sense for Lavos to have an "eye" on the world rather than magically be able to parse through good and bad DNA characteristics while hanging out in the core of the Earth.
This is the essence of what
descended from the heavens
in the prehistoric age.
The living crimson stone...
the Frozen Flame!
The Frozen Flame is the essence of Lavos. Having seen that phrase used in other video games by Square, it's safe to assume it is the life force or at least energy of Lavos (and probably only a part of its energy). If this is true then it's compelling support for the Frozen Flame being an intentionally made object, one which can change how it looks, interact with Lavos, and manipulate people. It manipulated Serge's father and turned him into a demi-human, it is logical that it could also manipulate people's DNA a bit at a time over a period of generations. Humans would discover the Flame at some point in history and it could be right there as mankind evolves. How does the Flame monitor the changes to all humans and determine which are best? How does it know if someone living miles away has the best genetic makeup for a certain trait? No idea, this is never explained, but if an advanced being is going to monitor this somehow, it makes a lot of sense for Lavos to be near the area, rather than thousands of miles away under rocks.
My second theory is that the Frozen Flame did in fact end up in the Mammon Machine. Someone would find the Frozen Flame and presumably it would be affected by it, maybe even becoming more powerful right away (if it was the Flame itself that caused the evolution of mankind then it has shown the ability to affect people immediately or gradually, which appear to be intelligent and sentient choices). It's totally possible that others nearby would be influenced as well, even if it took a while, but a certain group of people would stand out among the rest of the people on Earth. Eventually you would have a kingdom of people with an advanced genetic makeup...the Kingdom of Zeal. With the Flame in close proximity they would be smarter and it became manifest that they had magic powers while the Earthbound Ones, who weren't in close proximity to it, didn't have any powers. Yeah, the Sun Stone probably had to do with it too, but the Sun Stone didn't help the people individually stand out.
However, the unforeseen
coming of the mighty one from
the heavens suddenly smashed
their kingdom to pieces.
That one was known as '"Lavos!"'
The great crimson flame......
Wielding absolute power,
Lavos buried the dinosaurs -
the kings of the land -
in the space of a night.
However, the timid '"apes"'
who had lived hidden in
the forests...
...came into contact with
the crimsom flame
that fell from the sky,
and evolved into '"humans."'
The Frozen Flame evolved us from our basest form to humans.
In the eyes of the Dragons,
we humans are the foes...
A brain that has developed abnormally
to 3 times the original size in the
span of 3 million years...
We humans have evolved at an
enormous rate because of our
contact with Lavos's flame...
In a sense, mankind is Lavos's offspring...
You don't need to physically touch a substance to have contact with radiation from it. A number of people have had physical contact with it, I'm sure, but I don't think all the Enlightened Ones touched it, so I think proximity is all that's needed.
I think the only thing known to be able to contact Lavos, the Frozen Flame, was placed in the Mammon Machine. Mammon describes material wealth or greed, and the Frozen Flame is said to be able to have special powers and grant eternal life to the bearer. The Flame corrupted Serge's father and it also corrupted Queen Zeal, extra support that it was in the machine. Schala could interact with the machine but didn't have to touch it, didn't have to physically contact it. It got sucked into the void, which brings up the question of how it could be around later if it was in the Mammon Machine. Simple. Lavos makes another Frozen Flame. Lavos survived traveling through space and gamma radiation, a super powerful impact with the planet, it can create enough power to completely decimate the surface of the planet, it may even have the power to manipulate and transform DNA...creating another object or using another one to interact with and putting some of its power in it shouldn't be that hard for it. Heck, right after Lavos kills Crono another Frozen Flame could have been left at that place. The Kingdom of Zeal crashed into the ocean, creating a massive tidal wave, sending the ruins of the Kingdom, and another Frozen Flame, to the 4 corners of the planet. The Frozen Flame could have ended up anywhere. When you go to Last Village there's a woman there who makes an interesting comment.
A few "Enlightened Ones" did survive.
But no distinctions remain between the
"Enlightened" and the "Earthbound"
anymore.
Where did their powers go? The people were lazy, dreaming and sleeping each day away. Using magic was still part of their DNA but all the work was being done for them. They had the power of Lavos magnified through the Mammon Machine, it must not have taken any effort to cast spells with that much power around.
The Mammon Machine?
You came to see it?
Yes.
No.
I thought so!
Feel the flow of the mighty Lavos's
power?
Oh...I feel faint.
Oh, but you MUST feel them!
The last of the great Lavos's
emanations!
The power and energy of Lavos was all around them there, but that was gone and they couldn't cast spells on a whim. The Frozen Flame could have been thousands of miles away or perhaps not even recreated yet. It doesn't need to show up in the timeline until some time before Belthasar finds it around 2300 AD.
My third point is that Lavos allowed Crono and friends to attack it. In the battle with Lavos' outer shell we see it change into a bunch of different modes. All of those forms died, except for one, which was Magus. It's safe to assume that if Lavos would not have shown up then Magus would have been killed by a group of heroes looking to stop the person they thought was responsible for creating Lavos and an angry frog man looking for vengeance against the person who killed his best friend and transformed him. Lavos could have seen Magus die in the timeline and then interfered at that moment after gaining the information it needed from Magus. It seems that Lavos learns from the things that it sees die. It incorporates beneficial things from them after they are dead. So when it saw in the timeline that Crono and friends were the biggest movers and shakers out there, and they were coming after it, so it waited for them to become as powerful as they could and let them attack it. It could have wiped them out in 12000 BC but didn't. It gave them a chance to live and they came back stronger than ever. The perfect genetic specimens, and a wide variety of them too. Unfortunately I see some potential flaws in this idea, so maybe some parts are true, but not all.