All right, I apologize sincerely for posting on such a long dormant thread, but I hadn't seen it before, and it just now caught my interest.
Firstly, in regards to the religions and calenders (which, in topic, seems to cross over with the thread relating to real world influences), I would say that almost certainly Guardia is Christian, and thus so is Crono (or, at least, in name). As you have said, the calendar is based on the Christian one, the years being counted in AD, ie. Anno Domini, the Year of our Lord, which is a distinctly Christian measurement (at least in so far as measuring from the year 0 occurs). Thus in all of my own writing I portray that land as fundamentally Christian. I would generally agree with what is said here concerning the various religious affiliation that appear in Chrono Trigger/Cross. (Though I go so far as to hypothesise that the Chrono universe is, until about the year 100, little different from our own, save that a great continent lies in the mid-atlantic. During the time of Rome's persecutions a centurian, turned to Christianity, leads his legions across the sea to this island, which he then calls Guardia. This all makes Chrono Trigger more of a parallel universe to our own, and keeps many of the historical events of our world, such as Greece and Rome, and ancient Egypt. A true historical split would then occur at about 600 with the appearance of the Mystics, presumably in place of the Islamic religion which arose at around a similar time.)
However, I do have a comment or two in regards to Chrono'99. I would like to point out that the Giants being portrayed as lizards is likely a very localized myth, believed in only a small portion of Greece (as so often occurred); I, for one, have never read of the Giants being so, and I have read quite of bit of Greek myth. What I know is that very often the myths were multi-faceted, and varied from city-state to city-state, and region to region. Generally they were multi-armed and headed, but not lizard-like. Also, I did some checking on the spelling of Cronus/Chrono in my dad's Greek-English Lexicon, and I found something interesting. True enough, Cronus, the god of the golden age, is spelled with a kappa. However there is a verb form that comes from the name, and that verb is used to signify something that has passed, I believe (I'm guessing this comes from Cronus' reign having been completed and passed on to Zeus); so from that, I would assume, comes the word for time, spelled with a chi. Thus I think the idea of Zeus' father Cronus is actually a godlike manifestation of the concept of time. Janus actually bears passing resemblance to Cronus himself. For it is Cronus that weilds a sickle (with which he castrates the sky, at the behest of the Earth); later, in Roman myth, Cronus is identified with Saturn, that is father time, and he carries a scythe and hour glass. Janus, in the Roman myths, is the equivalent of Uranus in Greek, though there is no hostile takeover: he relinquishes his governship happily.
The myths seem to coincide at times, but the reason is not that it was intended that way, but rather the same reason that Tolkien's mythology is so similar to actual myths and events: he wrote his stories in an applicable way, and parallels, though he did not intend them, are easily made. He said so himself. In the same way Chrono Trigger, by drawing on the basic foundations of myths and legends in its stories often inadvertently parallels them. Though I would caution against the parallellisms that are brought up with Crono and Cronus; that is shaky, at the best. There is far more making Crono and Cronus different than similar. Cronus, for example, was not only a tyrant, but least of the Titans; yet it is in exchange for his facing of Uranus that the others make him their leader. He is fearful of losing his power, and not very wise.