Timeless Richard Theory
This may have been brought up before, but...
Ben seems very surprised that John is alive and gives the "dead is dead" line to Sun. We, however, have seen this before in regards to Christian, who speaks on Jacob's behalf. John seems to know things without any good explanation (Temple location, go to the basement, ect.) which implies at least an island connection and maybe a Jacob connection. Since Richard doesn't answer to the "human" leader of the others at any given time, doesn't age, and may be able to appear at will on the island (as to James and Kate), my theory is that he also arrived on the island dead, probably on the Black Rock and was reincarnated by the island.