*Cracks knuckles* Time to get back to work.
Okay, here's how things look, now that I come back to it:
1) Time travelers can apparently change the present from the past in many ways, even through seemingly insignificant actions (ie. Porre Mayor).
2) If the universe were inherently self-correcting in all manners related to time travel, the whole defeating-Lavos-to-save-the-world thing suddenly becomes pretty futile. The overall theme of the game is changing history; it wouldn't make sense for there to be a self-correcting mechanic like this, unless it were explicitly stated somewhere in the game or its sequel.
3) The Sun Stone can be brought back in time and placed in the Sun Keep in 65,000,000 BC. In the nearly 65,000,000 years until you can check it again, in 12,000 BC, it isn't disturbed. If history did have a self-correcting mechanism, it would surely have been able to act by then, wouldn't it? A convenient earthquake or cave-in could destroy it or knock it out and into the ocean.
Putting 1, 2, and 3 together, it seems obvious that a self-correcting law regarding time-travel can't be our answer here. But, we then have to explain how both Kino and Marle can travel to the future and meet their descendants. Here, I can think of two possibilities:
1. Partial self-correction - The event of a time traveler exiting the timeline to travel to a different point is the only possible time-traveling event that will cause the universe to try to fill in the gap and correct itself (note that if they go to the past, this will be completely unnoticeable). So, if they go to a future, it will be one that underwent the self-correcting process, but correcting only for their absense.
2. Genetic Averaging - Over the timescales we see the paradox taking effect, the other people contributing to the descendant's ancestry comprise almost all of the contributed genes. The change of only a single person in the past would be such a minor change that the descendant would be virtually no different.
So, let's look at our two cases: Kino leaves 65 million BC, and meets his descendant Marle. The universe has had 65 million years to correct itself, so the Guardia line could easily have been created from a slightly different ancestry. However, with all the generations involved, a single different ancestor 65 million years ago would have no noticeble effect whatsoever. It's possible that Kino's (and maybe Ayla's) place in the ancestry was simply replaced by someone else.
In the second case, of Marle going to the future to meet her eventual descendant, Doan, the same situation basically applies. The Guardia line could have simply been continued by a cousin of hers or something, who would already have pretty similar genes. The timescale isn't nearly as long, but it's still around 50 generations. This means that Doan's ancestry would differ by a minimum of only 1/2^50. 2^50 is on the scale of 10^30, which is much greater than the number of genes any person has. This means that chances are, not even a single gene would be different.
3. Preset Future - This is the other theory I hypothesized earlier, regarding traveling to the future. Basically, if you make a time jump to the future, you come to the future that would have occured had you not left the timestream at that point (that is, the future as if time travel had suddenly stopped working). When they return, the other version is Time-Bastarded out.
This last option now seems the least likely, as you'll note that when Crono & co. leave 1000 AD the first time, their absense is very much noticed. Additionally, this type of mechanic seems to lend itself too easily to paradoxes in the case of repeated time travel.
Theory 2 also faces a problem due to Chaos Theory - a small change in the past has a very good chance of causing large changes in the future in many ways, as the changes ripple out. In the end, I think our best bet is to combine theories 1 & 2. We have genetic averaging coupled with the universe trying to correct for the change. This should account for everything we observe in the game.
