Well the designers of Chrono Trigger handled it quite well. I think they should have skipped the time compression stuff and found another plot if they werent going to be detailed in their explinations. Though I'm probably very biased.
Hmm, I LIKE Chrono Trigger. Somehow I like it better then any of the final fantasies (which is odd, as I'm not THAT impressed with the SNES generation) but IMHO it doesn't concern itself much with logical consistency, concentrating on good clean fun.

When Marle 'kills her own grandmother'so to speak, the suggestion is that there's one timeline, and you can alter it.

On the other hand, on other occasions, whatever the heroes do ends up causing what happened in teh first place anyway. Magus being defeated, The Reptites defeated...

Also, at the end it gets really confusing. With Doan, who should be gone, as I can't imagine the future being just the same with the day of Lavos averted, unless you're gonna start messing with parallel universes.

Besides, I happen to think FF VIII has dealt quite well with the time travelling stuff....Sure you get paradoxes, but CT has those too. (If Marle was never born, then how did she interfere with herself being born in the first place?) Actually, FFVIII avoids the paradoxes, as nobody has succesfully altered the past at all. (Ellone tried to keep Laguna with Raine, Ultimecia tried to destroy SeeD that was destined to defeat her)