Okay -- so, the systems. The votes and my own internet research put three systems near the top for my purposes: 1) FATE (Spirit of the Century version), 2) Some d20 system game (D&D 3.5 and Pathfinder voted for, True20 often mentioned online) 3) Savage Worlds. So -- as I'm trying to make this salable, I'm going to stick (for now) with the free systems, which cuts Savage Worlds out. And then d20 -- Pathfinder and D&D 3.5 are just simply too magic-heavy and medieval for my purposes, so I'm going to have to go another way. The question now is d20 Modern, which is perfect for low-magic and has very similar rules to D&D 3.5 but is less well-known (and apparently there is a lot of argument on various forums saying it's unbalanced -- I never noticed that, but I'm no rules lawyer) -- or True20. True20 is arguably more elegant and has an interesting magic and damage system that fits Terra Incognita's themes, but has no free System Reference Document, so while I can publish under its rules system for free, anyone who's not already running True20 would have to purchase the book (as opposed to d20 Modern, which has a free SRD online). Additionally, True20 is quite a bit different from D&D/Pathfinder, potentially causing confusion in the readers/players. And once again, I don't know which one is more popular.
And for the world:
Races/Creatures: This is a campaign where most, if not all, of the PCs should be mundane humans (at least at the beginning of the story). However, for GMs who decide to be contrary, and for PCs entering later (new players, players whose characters died), we may want rules for various supernatural creatures as PC races. And certainly, a few supernatural species are likely to dominate the campaign world, becoming recurring, if not ubiquitous, allies and villains.
The most important supernaturals are, of course, the Atlanteans. Corrupt, arrogant, imperialistic and paranoid, they are unlikely to be suitable as anything but villains. Then again, that's what they said about the Drow before Drizzt Do'Urden, right?
After the Atlanteans, the most powerful species are the Fae. These are not D&D elves here -- I'm taking inspiration from the oldest myths and recent interpretations (Discworld, Changeling: The Lost) that emphasize that the Fae are alien, incapable of understanding humans or their morality. They may often also feature as antagonists -- but they are also capable of being allies, as they don't like how powerful the Atlanteans have become.
Though not powerful politically, the Cyclopes/Kyklopes are nigh-ubiquitous since the Atlanteans enslaved them all. They act as the Atlanteans' grunt troops as well as physical laborers, and those small pockets who've managed to free themselves are likely to show great kindliness to the PCs (once they definitively prove they're not Atlantean).
I feel conflicted about Satyrs, Nymphs, and Centaurs. All are interesting creatures, and it would be intriguing to explore their cultures. However, I don't want to overload the world with all-Greek mythology, as the central conceit is that all myths are true.
A few other creatures worth mentioning, mostly as enemies (most of which I used in the original campaign run):
Grendel's Children: Yes, so what if Grendel and his mother died in Beowulf? What if Grendel had, as well as a mother, a widow? What if Grendelkind have litters? By the 16th century, there could be a small population in the hundreds or thousands, hiding in the depths of Denmark, continuing to quietly massacre villages.
Fir Bolg/Tuatha de Danann: Two sides of the same coin, the Fir Bolg are, according to legend, the original inhabitants of Ireland, a savage race and, according to my take, hideously deformed mutants. The Tuatha de Danann are the interlopers, godlike "perfect humans" who were later worshiped by the Irish. Who's the hero and who's the villain in this piece is up for debate.
Jotuns: The Ice Giants of Scandinavia, the Jotuns (YO-tuns) are the traditional foes of the Norse gods (especially Thor). Unlike the Cyclopes, they are often seen to be civilized and intelligent, if rather too focused on destroying the gods and bringing about the end of the world.
Tritons: Children of Sea God Poseidon (as the Cyclopes also are), Tritons are the archetypal mermen/maids, and rule under the ocean. They are likely to fight the PCs, but could also be reasoned and bartered with...
And a host of other creatures abound in mythology, ready to be plopped in with a minimum of fuss, including: the Ankou (British), Baba Yaga (Russian), Banshee (Irish), Black Dog (English), Catopeblas (Ethiopian), Cerberus (Greek), Charon (Greek), Chimera (Greek), Djinn (Arabic), Dryad (Greek), Ghoul (Arabic), Drude (Germanic), Fachen (Scottish/Irish), Gorgon (Greek), Harpy (Greek), Hobgoblin (English), Hydra (Greek), Ketos the sea monster (Greek), Kraken (Nordic), Leprechaun (Irish), Leviathan (Biblical), Homonculus (Alchemical thought), Manticore (Persian/Greek), Minotaur (Greek), The Nuckelavee (Scottish/Orkney), Red Cap (Scottish/English), Roc (Persian), Scorpion Men (Babylonian/Sumerian), Selkie (Irish), Siren (Greek), Svartalf (Norse), Talos the Automaton (Greek), Tengu (Japanese), Troll (Scandinavian), Umibozu (Japanese), Werepanther (African), and Will o' Wisp (English)
So you see, there are a lot of options. Next time, I'll examine the unusual role of magical artifacts in Terra Incognita