The major thing on my mind right now is what to name the Ancient boss in the first 11,998 B.C. scenario. My first thought was Baal, after the pagan god of fertility so ubiquitous in the Torah. Either that or Molech, the other pagan god most frequently mentioned -- the Bible records that worshippers of Molech sacrificed even children to their god. However, both of those names have been yoinked already, so I'm a bit hesitant to use them without discussion -- Baal for the Diablo series, and Molech for Buffy the Vampire Slayer. I would advocate the usage of Cthulhu, except that Cthulhu is too similar to Lavos -- not to mention that most people know about him. They'd expect Cthulhu to be this insanely hyper-strong monster that nobody could beat, like Draco'dur in World of Warcraft or Uber Diablo.
Then again, we do need one of those as the obligatory optional boss for late in the game. Thoughts?
Well, Baal is simply 'lord', as I think you know. So, Molech is out? How about Mot, the Caananite god of the underworld? Too short probably.
Just be careful that you don't take something from myth just for the heck of it. It's okay to some extent, but gets obsurd when it comes to something like Xenosaga's 'Nephilim' which, at least as far as the first game portrayed, bore absolutely no resemblence at all to the source of the name; an ethereal woman can hardly be described as a giant, or a fallen hero of old, after all. That's just sloppy storytelling from people who think it cool to throw in Biblical/mythical allusions for the heck of it, but leaves those who actually know it scratching their head. Xenosaga seemed especially bad for that, actually.
Anyway... names... well, if it is some ancient lord, just about any of the gods of the middle-eastern regions will do. I'll rattle off as many as I can remember: Tanith, Astarte, Enlil, Enki, Tiamat, Marduk, Ea, Apsu, Anu, Ishtar, Innana, Kishar, Anshar, Qingu... you could probably get this if you went to the Encyclopedia Mythica, you know. I'd suggest looking there through the list of god's names till you find one that catches your eye, and then check to see if it is at all similar.
Also, and this can also be looked up on the Encyclopedia Mythica, perhaps for a Hellenic connection, some ancient Greek titan may work - although the more eastern names would likely be better. Just for suggestion's sake, I'll see if I can remember a few... One of the Hundred-handed, perhaps (they have a Greek name I cannot remember at the time.) There is also Atlas, though he is quite well known. Okeanos, the Sea, might be alright, depending on the nature of this ancient thing. Typheous (the y is actually ü, I think. And the spelling may be a little wrong...) He is last of the Titans, whom Zeus himself fights with the sickle of Kronos. Hesiod gives a full list, but I think Theogony went back to the library already, so I can't look them up. There are a bunch that are ancient gods, but aren't considered Titans, like Styx, or Erebos, Night, etc.
Furthermore, if you want something connected to ice, I'd think that, although the sound is different, Norse would likely have more of that sort. Ymir is the great ice giant, killed by Odin and his brethren. Thrym is another ice giant, I think, and Skadi, his daughter, though she marries Njord of the Vanir, is also of that kin and of a more chill-windy nature.
As far as other made-up names... those don't have the allusive history behind them (and in RPGs, cleverly done allusions are very good, indeed. I'd think it one of the hallmarks of CT, as well) but, seeing as ZeaLitY seems to have started in that vein, I'll try as well. To me, made up names must always have a meaning, so I'll try and wrack my brain to see what I can remember from all the words/names I've made up in the past. If the motif is to be ice, that is 'tryst' to me, so... hmmm... ancient is 'nemoth', but that doesn't exactly match. Let's see... Trystel, Trystanos, Heltryst, Heldain, Trysteth, Tiamtryst, Heldiom... no good ones are coming to me. I would need my language's dictionary with me, and they've got all more northern sounds, anyway.
I'm thinking that the ancient ones can appear in the Chrono Compendium library at Chronopolis as well as in the game. The Rainbow Shell could be the shell of a great, ancient nautilus, crushed beneath Lavos's weight and its materials refined in the heat. I've got a name for the enemy near Magus -- Glacek. At first, I was thinking something with a hard K sound, like Kracious, and the ice motif returned to me. I was able to integrate that k into the sleekness of "glace." What do you think?
If that's how you'd wish to pronounce it, then I'd recommend using an s in the place of the c. I've got something of a dislike for that letter, as it causes endless confusion in most fantasy names. So it should probably be spelled Glasek to avoid confusion.