1-Why did Marle Disappear when Lucca first arrived at the Middle Ages?
It wasn't Lucca's arrival that caused it; Marle being sent back to the past caused the Guardia Kingdom to call off the search for Queen Leene, who had been missing(abducted by Yakra). In the original timeline(the one that existed before Marle disappeared) Queen Leene was found at the cathedral and Yakra was defeated, and so she lived to have children. Since the search was called off after Marle was found, Queen Leene would have never been rescued, and therefore, not lived to produce offspring who would later become Marle's ancestors.
I disagree!
This is known around these here parts at the "Marle Paradox" (not to be confused with the Guardia Paradox). It is a point that the compendium's traditional theories have been unable to address. You can see a discussion of a lot of these problems over in the TTI/TB/TE Reformation Idea Collection thread (
http://www.chronocompendium.com/Forums/index.php/topic,6845.60.html)
First, the timeline does not change based on WHAT might happen. That is, as long as Leene was alive, we cannot say that her not being rescued because Marle was there resulted in Marle disappearing. This would create a paradox anywho; if Marle's presence caused the search for Leene to be called off, then Marle's disappearance should have called it back on, with would have resulted in her reappearing, which would have resulted in it being called off, which would have resulted in her disappearing, and so forth.
Second, the timeline changes seemingly immediately. We don't ever get to see the full process of a time change, but as soon as you change the past and warp to the future, the future is changed. There seems to be no delay between a change in the past and its affect on the future. Thus, as soon as the search for Leene was called off, Marle should have disappeared. That she did not disappear then indicates that more than the search was important.
Third, we know that Frog was still searching for Leene despite Marle being found. He knew Marle wasn't Leene. Thus, in all likelihood Leene would have still been found.
This is as far as we can go based only on what they game tells us.
We can speculate, however. My own speculation is that something about Lucca's presence in 600 AD caused a definitive decision to be made (definitive enough to have the same weight as action) that resulted in Leene not producing royal heirs. This was then counteracted by a subsequent definitive decision that was made shortly after Leene returned to the castle (as soon as Leene was saved, Marle should have reappeared but there was a cinematic delay). Thus, given Frog's persistence in finding Leene, his disgrace after her return, and the alternate ending where Marle is frogish in nature, I conclude that something about Lucca being present in 600 AD caused Frog to decide to rescue Leene and
run away with her. That decision resulted in Marle's disappearance because Frog's decision was as good as gold and better. Marle reappeared because Crono and Lucca's influence foiled that plan and that decision became impossible.
Whatever the actual reason, Marle disappearing because of the search being called off makes the least sense.
2-Having Ayla wander through the ages, wouldn't affect the course of things, considering that she at the end returns to Pre-History, but she already saw everything that happened, so she could easily make profit of the things she learned from the future.
First, you are touching upon the Guardia Paradox (the entire guardia line should disappear when Ayla disappears, for the same reason Marle disappeared). She returns to pre-history, true, but until she actually does so, her return can't be taken as having happened (unless, I suppose, her decision to do so was as solid as Frog's and there was a significant degree of inevitability about it, as per my speculation above).
However, that aside, you are forgetting that she only knows humanity's future, not her own. She doesn't learn how to use any technology that her people don't already have (and don't forget, they have guns!). How could her knowledge of the future then be put to use for fun and profit?
4-Defeating Lavos in 1999 erased the future we saw in the game, right?But all past events(pre1999, like the fall of Zeal and etc) still happened, right? Would it be possible that in the future created by killing Lavos, if someone created a time machine capable of transporting big stuff, to take a weapon powerful enough to destroy or at least change the course of Lavos so he wouldn't hit the planet?
Sort of, but it would be highly dangerous to do so. Let us say that Belthasar from Chrono Cross did this; Lavos is deflected, he never falls. The reptite win the war with the primates, humanity never creates a civilization, Belthasar is never born, he never creates the weapon to deflect Lavos, so Lavos falls and we repeat. Too bad the Chronoverse doesn't have some sort of race of cool aliens who have mastered time travel and created laws regarding such to prevent paradoxes like this. url=http://en.wikipedia.org/wiki/Time_Lord]Time Lords, if you will.[/url]