It's so hard for me to keep reading debates about how discrepancies are actually clues to explanations after reading this:
"You've said many times that when people find out who Adam and Eve are, we'll all realize just how long you've been planning the mythology. Well, I went back and watched the "House of the Rising Sun" scene, and Jack says that the clothing looks like it's 50 years old. Is he just not very good at calculating the rate of decay on fabric? "
CC: Jack is not really an expert in carbon dating.
DL: He's not really a forensic anthropologist. We need to bring in Bones.
CC: Or Charlotte. She's an anthropolgist.
DL: The other theory that I would like to throw out there is that Jacob and his mother were just expert craftsmen. They made those clothes on that loom so well, it would appear that they were only 50 years old in decomposition, when in fact it's several thousand.
CC: Or perhaps the fabric is magic. A lot of theories there, Alan.
These writers are good with the magic fabric explanation. (yes I realize that it's tongue-in-cheek, but it's also clear that they don't care, as long as they never have to admit that they didn't plan for Adam and Eve to come from long long ago. Why they can't admit that I don't understand; it hurts them more in my eyes that they have to descend to silly banter to keep up the illusion.
If they did know back in Season One that the bones were MIB and fake Mom, then there was no reason to put in dialogue where Jack came up with an estimated time for the clothing. He could have just said that they looked "real old."
In any case, there shouldn't have been any fabric unless the power of the island has a special interest in preserving textiles. No, but then the fabric shouldn't have been decayed at all.
The simplest explanation is usually correct, says Mr. Occam as he shaves, and that is that the writers either hadn't worked out the mythology, or that the skeletons were originally someone else in the group who had time traveled.
I'm fairly sure that the Adam and Eve discovered in the cave had their hands clasped, and we inferred they were a couple, whereas they didn't bother to have Jacob stage this. It wouldn't have worked well with the final plot where MIB whacked Mommie Dearest and Jacob was totally jealous of their bond.
In some podcast from long long ago, Darlton said they had planted an anagram that said who Adam and Eve were, and fans found an anagram that worked out to the bones of Nadler -- Rose and Bernard.
`If there's no meaning in it,' said the King, `that saves a world of trouble, you know, as we needn't try to find any. ~ Lewis Carroll