Here's my theory if anyone is interested.
It's a power struggle between two (or more) Egyptian gods. Jacob is Sebek-Ra. Sebek-Ra is a composit of Sebek and Ra, a manifestaton of the sun-god. In this role he was envisaged as a man with a crocodile's head (think colossus holding an ankh in each hand). At the begining of the episode we see Jacob weaving a tapestry of the sun with tiny people bowing down to it. The guy on the beach in the black shirt who said he wants to kill Jacob and will someday find a "loophole" is Apep or Set. Apep/Set is depicted as a snake-god, the serpent of chaos and is opposed to the sun-god Ra. So, I think Apep is the smoke monster and can take on the appearence of anyone, in this case the permenantly dead Locke. I don't think Ben is Apep's loophole and I don't think Jacob/Sobek-Ra is dead. But I'll have to wait until next season.
The goddess Tauret could also be - or was- at work on the island. Tauret is the goddess of childbirth, depicted as having the head of a hippo, the legs of a lion and the tail of a crocodile. Her fearsom appearance drove off evil spirits at the birth of a child. Perhaps this goddess left or was banished from the island. This coluld be why no-one is able to conceive on the island, except for Sun, but Jacob personally chose her and Gin
-edit Jin-. Clair
e and Rousseau conceived before they came to the island. Eloise is a good candidate for Tauret or perhaps another character not yet revealed.
Cerebus
-edit Cerberus- was metioned as well and old Vincent doesn't seem any worse off after all the time shifts and such.
The magnetic anomaly is a wormhole. The Oceanic Six took off from Sydney to LA. They were off course by 1300? miles so this would make the island somewhere in the southwest Pacific. If I could dig a hole from Egypt (Thebes or Karnak) I would come out on the opposite side of the planet somewhere in the southwest Pacific. Same with Tunisia but the antipode would be a bit more south
-edit and east- since the island moves
-edit and Tunisia is north and west of Egypt- .
The colossus could have been built by the slaves and crew of the Black Rock. I think Richard was the Captain and was thus given immortality by the gods since he doesn't seem to age.
Or not to all the above.
Anyway, I could go on and on but ancient Egyptian mythos is so convoluted the writers have a perfect subject to use their creative licence.
Edited for clarity and spelling....hopefully.