The whole Atlantis thing...why would that have to be the explanation if it was an ancient civilization? I don't think it's Atlantis, but more of a tribal, Lovecraftian culture built on the island from the inside out. Since we know the island can "move", the civilization must have been completely inclusive.
I think the forces on the island are truly supernatural, and unexplainable. There are many such places that actually exist, where physics and science sort of twist.
The ancients must have developed the wheel, the room I am SURE is behind it, the statue, and maybe the smoke monster (although i think that thing is from another dimension or something). They lived in harmony with the island's forces instead of manipulating them like the D.I., and I think that's what the Others are fighting to return to...the ancient's way of life.