I just watched the finale today so here goes...
Osiris and Set or God and the Devil, I think in the end it's obvious that there is a "good" being and an "evil" being and the whole thing has merely been a struggle of good vs. evil.
At first I couldn't figure out which one was good and which one was bad. Then I was convinced that Jacob was the bad one for several reasons. In bible stories and such it is always the devil who tempts people, or tries to push them in certain directions and God usually stays out of it. But then it dawned on me that Jacob was there, in a lot of moments that helped people out and he was trying to ensure that they would all make it to the island because for one reason or another they deserved to be there. And then at the end the other guy kills him so now it seems even more likely to me that Jacob is/was good and the other guy bad.
So here's my theory, it's very biblical but hear me out. The island is the garden of Eden. Jacob (or God) wants to bring people to the island so that they can be happy and all that, since in the conversation with the other guy at the beginning the other guy asked him why he keeps trying to bring people to the island. But human nature being what it is, no one on the island is ever content and they end up fighting each other (apparently over and over as the other guy mentioned) and in one way or another people are banished and not allowed to ever come back (Adam and Eve).
Also, Jacob brought the Black Pearl to the island which was a slave ship. If anyone deserved to be in paradise it would have been the slaves on that ship. Also if Richard was the captain of the ship (as some one said previously) his punishment could have been to always be in the service of Jacob and to act as the middle man between him and the "leader" and that's why he never ages.
Now the ending, where black turns to white and white to black. That kind of threw me since white is good and black is bad right... but I think that it just means that the situation will now be the opposite. For now Jacob was running everything and even though it all seemed so bad (black background) the intention was really good (white logo) and now everything will seem good on the island (white background) but really things will be controlled by the evil guy (black logo).
Anyways, it's far out there and I have no idea what they could do with this next season but that's my theory.