The fact that the Elder is so intent on wiping out the vampires suggests that he may in fact have been worshipped by the Hylden. Think about it, who built the chambers which housed the Elder in SR2? It's implied in the game that it was the Ancient vampires (granted they built at least the pillars in the subterrainian chamber and added the frescoes) however it seems more likely that whoever actually worshipped the Elder built them. First of all there is the chamber with the stone effigy of the elder, which looks like a sort of idol or form of statuary worship. In fact the layout of all the subterrainian chambers gives us many clues as to their possible use and who built them. The caverns north of the Elder's chamber (the still rough cambers but with carved out stairs) look to be of the earliest construction (and of a fairly organic appreciative aesthetic society).
These then lead to the chamber with the effigy of the Elder, whose large open construction, huge bonfires, and central location of the idol look very much like an area of mass worship. Through still more tunnels we reach the Elder's lair with the exalted one himself very present :-)
This configuration can be seen in many real world temples (especially those of Egypt) where the masses (or public) are permitted only to worship the outer facade of the holy area whereas the initiated priests and select few dignitaries are permitted to enter the inner sanctums and (in this case especially) view the god in it's true and literal form.
As for who these worshippers were, I believe it to be the none other than the Hylden, for two reasons. The semi organic look of their architecture we see in BO2 (which in that case was a machine and therefore primarily focused on function rather than aesthetic value) would perhaps translate into a more completely organic form in their temples (as sites focused mainly on aesthetic appeal), which we can see in the chambers. Secondly it is obvious that these chambers have been there for perhaps thousands of years, making the Hylden the only logical choice.
I suggest that originally the Hylden worshipped the Elder god here and that at that time only one entrance existed to the caverns (the swamp end), however as the war with the Vampires progressed the pillars were constructed and driven down through the Elder's chamber (and body) effectively pinning him in place while also acting as a seal against the return of his worshippers (having been banished to the demon dimension). With their enemies defeated the Ancients set about converting the chamber, adding the murals of their victory and excavating their own entrance (decking it all out in their gothic type architecture) in anticipation of Raziel in his journey as the 'savior' and so on.
One thing that puzzles me though in my theory (and it's a really minor fact but still annoying) is a small (and easily overlooked) carving in the Sarafan Keep around one of the hearths (where tons of Sarafan Knights hang out). It shows a man (or soldier or something, at least humanoid!) holding a harpoon, with a tentacled creature below him. It's a bit of a vague description I know, but I haven't seen it in a while. This puzzles me as it seem to indicate that the Hylden, or at least the Neo-Sarafan are enemies of the big squid we all know and love (or loath).
Anyone else have any theories?

