the skull has been left pretty much unscathed so far, so I think we should start talking about.
I'm pretty much positive that it's the skull of a Visitor (octopus things), because of the 3 eye sockets. the only weird thing is that the eyes are oriented differently than they are on the skull, but if you look at the bottom of it you can see 3 more sockets; most likely for the tentacles.
you could say that its purpose is to foreshadow the ending, but I have a feeling it could play a part in solving THE BLACK MONOLITH(!).
first of all, the achievement for it: "The seat of knowledge is in the head." is definitely peculiar. we already saw that the achievement for the tome hinted that it was a book of haikus, so that's something worth thinking about.
second, the eyes. the Visitors have 3 eyes, whereas everything else has 2. you need 2 eyes to perceive depth, so what happens when you have three (in the context of the game)? it could be that the key to the monolith has something to do with the 4th dimension, be that time or spatial (probably the latter).
having met Fish and attended one of his panels about FEZ, I can tell you that the dude is crazy about 4th dimension stuff (and he does a lot of LSD).
story-wise, it's likely that the Visitors came and created the third-dimension, or at least left the monolith and the concentric circles.
also don't forget that in 2001: A Space Odyssey, the ape threw a bone at the monolith.
wha'd'you guys think
I think you are probably on the right track. I also thought about the skull's achieve text. The seat of knowledge is in the head.
What does it all mean. This solution better be good, its taking long enough
"The seat of knowledge is in the head..." is part of a quote by British author William Hazlitt.
My sense of the Skull artifact was that it was just meant to show you that the skulls, faces (like the ones you see in the first area after the starting town), and octopus aliens are all the same--If you tilt it the artifact around and look at the bottom, you will see what I mean.