If Jacob has been watching MiB since the time of Richard Alpert, then why is it that now, he's looking for a "candidate to replace" him?
Simple answer: Jacob knew he was going to die.
For decades and possibly centuries that he's been watching the MiB, he's only looking for a replacement now because he knows the MiB has found his loophole. This is why he never even put up a fight when Ben was about to kill him. Jacob knew his time us up... but not without a plan of his own... Jacob and Ben has been talking secretly all along.
Back when Ben was the leader of the Others, he's always said that he's one of the good guys. If you guys remember carefully when he put Kate and Sawyer in the animal cages, he would make them work and build a runway. This is the same runway the Ajira Flight used to land safely back to the island. In which case, Ben "saved the other candidates" from dying if the runway was never built. He knew that someday that runway would be used by them. This is all part of Jacob's plan.
We all know how much of a great actor Michael Emerson is. I think that Ben and Jacob has been talking together since Ben started serving the island. No one, and I mean no one else cares more about this island than Ben. When Jacob told Ben about the plan, it requires Ben being shot at, beaten up, and be disgraced by other people. Ben knew all this would happen and this is the ultimate sacrifice Ben has made for the greater good of the island.
The way Ben has killed the real John Locke is also part of the plan by Jacob. When Ben killed the real Locke, he did say he was sorry that he had to do this. To me, it sounded like a sincere apology. So far, the real john Locke has died twice already in the show. once from falling off the building, and the other time when he was shot at by Ben Linus by the purge. If the real John Locke has already resurrected from the dead twice, I think Jacob has one more magic in him to bring him back from the dead. Maybe, the real John Locke IS the chosen candidate and what's the most perfect way to protect him from the MiB's influence than to bury him away and for him to "pretend" that he's dead?
I also think that the real John Locke will inherit Jacob's place. The real Locke loves the island, and he does not want to leave the island. How ironic would this be that MiB is being kept by the same person who's body he once had? Ben Linus will be the leader of the Others, since after all this, Locke knows that he will be able to trust Ben. Richard Alpert's time will also be up. Jacob promised him eternal happiness and I think Richard will be buried at the caves with his wife Isabella, with the black and white stones symbolizing his service to the game that Jacob and MiB has played for decades.
As for the other members, well. We'll see what the show will show us!
Namaste!