Has anyone posed the celestial envoy theory yet? That Lavos is in fact a galactic missionary that seeds the universe through itself and its offspring, intentionally advancing creatures from a world, and in turn absorbing those enhancements into itself to be spread to yet more worlds by its offspring? Perhaps in its own mind it is not angered by humans' advancement, but is in fact attempting to euthanize a species that is working itself harder and harder toward oblivion... Perhaps we, and the planet, simply don't understand these motives.
I've personally always believed that it was simply Lavos deciding its work was done and breaching to allow its offspring freedom on the surface, possibly as they could not yet withstand the heat of the earth's core.
I could also see that perhaps the fallout from Lavos breaching the surface is an unavoidable rain of destruction. Perhaps that is how it seeds a planet with its young. Perhaps Lavos was giving the gift of greater genetic diversity to a planet that had stagnated with only a single intelligent race surviving. (We don't see any Nu's apart from the robot Belthasar built in the future, nor do we see any obvious evidence of Mystics).
That said, it is entirely possible that it was still swatting a troublesome bug when it destroyed Zeal... after all, by previous logic, it could always revive life on the planet again later.
Another possibility is that the Frozen Flame, used in the mammon machine and later chronopolis, is not simply a piece of Lavos, but is a pre-natal form of Lavos' species, which may develop embedded in or shielded by the spines on its body... When it got separated, it was not concerned for it initially, as it is obviously a hardy species, and could presumably reincorporate the pre-infant Lavos seed/egg into itself for gestation later...
however, when humanity started using it to siphon energy from Lavos (Zeal) the energy transfer, specifically the high transfer rate experience in the undersea palace, was a danger to the offspring, and it destroyed Zeal to protect it. It then settled as there was no more immediate threat...
until later when Chronopolis gained possession of the Flame, abusing it further still, and so, Lavos decided chronopolis had to be silenced this time... But since it was less advanced (we can assume anyway) or differently advanced at any rate, Lavos could not outright destroy Chronopolis, and sent it into the past, knowing it would cause a backlash that would have to be met with retaliation on the part of time and the planet...
IE: Knowing it would give Chronopolis something else to worry about besides Lavos and the Flame directly. With the Flame in the past, it was still safe from the ravages of time, being not yet even a developing organism; still in stasis.
Another note is that I think we assume intelligence indicates a certain kind of behavior. I think it's possible that Lavos can be extremely intelligent, but not be directly sentient, or it can be very advanced, possibly intelligent, but not think in a way that is even comparable to us.
Seeing as Lavos has at least some form of temporal ability (its body is affected by all time periods simultaneously) it may think in higher dimensional planes than we, maybe even 9 or 10...
Most humans interestingly enough, only think in 2 specific dimensions at a time, with only some rather gifted people thinking in 3 at once...Perhaps it's due to the fact that we can only display 2D information, even if it represents 3D... normally. But Lavos' intelligence, if it supports, say, 4 dimensions... full spacial, and then time, and can think in all of these at once, it might be extremely intelligent, or maybe only nominally so, but still has a different kind of thought than we do... Something we could only hope to comprehend using oblique angles: thinking in 2 or 3 dimensions at a time... thus we could never fully understand why it does what it does, or how much it understands what it is doing.
On a similar vein, Perhaps Lavos is merely as intelligent as we, and thus it miscalculates and makes mistakes... maybe even frequently. However, it may, while not being supremely intelligent, have supreme amounts of knowledge... That is, it solves problems at our own level, but it has more information to use when solving.
This is the same thing that makes some scientists seem devoid of common sense, and some uneducated people be very good at strategy. Intellect does not equate to Knowledge nor Wisdom.
I fully realize my multiple points don't all mesh, and they aren't intended to, they are merely my various thoughts on Lavos' intelligence and motivation... Different possibilities.
