I'm not bringing this up to be a negative nancy, but there's an interesting hypothesis that half of everyone who's commented on Skeletons has to say about them which I almost want to believe, but can't reconcile with basic human anatomy. The theory goes that skellies had something of a T-800 thing going on; that what we're seeing are their metal endoskeletons once covered by fleshy bits.
At first this makes sense because of the Skin Bandits. Those geinbots wouldn't be doing their Buffalo Bill routine just out of gullability. I posit they play along out of desperate self-delusion; they go ahead with the scheme because they need it to be true. The opposite is commented on by Elder if one goes and visits him as a Skeleton oneself: the madman goes on about how Skeleton Bandits are willing to believe they can become robots in order to escape their miserable existence.
There is a flaw in the theory that Skeletons are meant to be Human roboendoskeletons, however. It's most obvious if you look at their feet, less so in regards to the rest of their anatomy until you look at the head; there's no way all that's fitting properly under a healthy coating of flesh and blood. It can't even fit under a coating of flesh and blood that's been run through a potato-peeler.
It could be argued, possibly, that over the years they had bits and pieces replaced with a set of standardised replacement-parts, perhaps during the Second Empire. The Great Chaos might have quite throughly wrecked anything delicate enough to fit under human flesh and the Second Empire were mostly Skeletons; so it makes sense that they might've had a number of standard replacements for less robust components, seeing as any semblance of being Human was (so I reckon) likely a pipedream by then. Their extremeties are the most obviously non-Human, with the hands having only four digits and the feet (being quite big) lacking any.
Of course, Okranites go on about certain people being robots in disguise, but there's a simple explanation to this; they're too indoctrinated to know what prosthetics are. Think about it: if you were brought up to believe that anyone, anywhere could be an Arnold, just ready to kill some unsuspecting human, your first thought upon seeing a human with a robot hand would be that it isn't actually human. If you read volumes one and two of The Guiding Light, one can determine the clear-as-day fact that The Holy Nation are willing to call anyone they find undesirable a Skeleton, and with a bit of speculation assume that they do not in fact know anything about skeletons aside that they hate them.
I did think for a moment that perhaps MK-II Skellies were the "original" ones meant for T-800 business, but their feet are very... odd. Their feet are this kind of U-shaped bar hinges at the forefoot and forms the heel, I suppose as a means of absorbing shock. I believe these are the same as Stealth Legs. It can be assumed that the name MK-II means that they were a later model built after the glory-days of the First Empire to produce Skeletons on a budget, but that's a different tangent of speculation.
Now, here's my own wacky theory. Skellies are robotic endoskeletons, but not of Humans. Rather, they have a spiritual common ancestor with Hivers of all things; both resembling a single, as of yet undepicted species. The first similarity I noticed with Hivers and Skellies is that they're on average about half a head shorter than Humans, but I also think there's some correlation between subraces of Skeletons and Hivers: Default Skeletons have wide upper-heads and are good at fighting, P4 Units are the brains with beady eyes and large craniums, Screamers have tall heads with eyes at the extreme sides, Soldierbots... I have no idea.
That I'm trying to express is that whatever species that Skeletons were skeletons of may have either had specialised sub-species like Hivers or they associated certain proportions with personalities and traits (wide upper-head means you're tough, large cranium means you're smart, tall head means you're of a servile demeanour, long head means you're good at shooting) which was later reflected with the creation of the Hives. Going by this theory, the Hive are also an offshoot or creation of the same species. The books Cultural Groupings and Evolution speculate on a "master race" which is perhaps this species.
I assume that if this species is what Skeletons and Hivers are based on that they would more closely resemble Skeletons and that Hivers are a (if you like) cut-down version thereof, perhaps made as slaves or a desperate measure to survive The Great Chaos. In that case, I can imagine them getting by on another continent and not showing up on the one the game is set on for quite a while. Remember, the ocean was higher in the past, there are ruined boats all over the place and hivers didn't appear until after the fall of the Second Empire; so it may well be that quite a bit was going on from then and the First Empire.
So in summary, my own terrible theory is that Skeletons are the skeletons of some unconfirmed alien species. It's not a good theory, it requires leaps in logic, but I thought it might amuse some of you at least. I'm at least curious to know if anyone else had the notion that Skeletons were built by Proto-Hivers.
A rather elaborate and well-put-together theory, but my guess is that things are much simpler than that - the appearance of Skeletons is just a design which the devs have decided to implement without actually giving second thoughts like that :D I mean, they may decide to explain this somehow in the sequel, but I think that initially the artist's task was to "make humanoid robots".