This is a theory I've been working on since the Season 5 finale in May.
Basically, the purpose of the Island is to judge humanity. Like reverting back to the original premise of LOST - "Lord of the Flies" as a TV show. Jacob and the MIB are two - well, for lack of a better word, lets call them immortals - who's job it is to judge humanity. Their bodies, as seen in "The Incident", are obviously not their original ones. They are just bodies they possess. But to possess a body, that person must be important, must have fulfilled some kind of requirement, to become a "candidate", like Frank.
These immortals have been on the time-traveling island a long time. The reason the island can time-travel, the reason it can manipulate time, is because it's original purpose was to be a vehicle and a stage for humanity's judgement. Jacob and MIB have probably lived through time, through the destruction/extinction of humanity over and over, each time time-traveling back to the beginning. Meanwhile, MIB is tired of this, believes the cycle will simply continue - he believes humanity is evil and will continue to destroy itself. Jacob is not so sure, and wants to continue and save them.
In Season 6, we'll see what happens in a different "cycle", ostensibly created b/c of Jughead. But the island is not changed (maybe we really will see 2 different Jacks on the island, if the ALT characters make their way to the island. In that case, "Exploding bunny time"). The actual variable is not people - it's Desmond. He can see through the multiple cycles, and is exempt from them. That's where he comes in during Season 6.
Tell me what you think of my theory.