Here's a question I get a lot: Why was Jacob able to leave the island, seemingly at will, but Man in Black was not? A related question is: Why did "Mother" and Jacob want to keep Man in Black on the island?
My answer, though there is no solid proof to this theory, is that Man in Black wasn't able to leave the island because Jacob made a rule that he could never leave the island. Man in Black tried to dispose of all the candidates so that there would be no protector of the island and then he would no longer have rules to follow. I think Man in Black had a hard time killing and getting rid of the candidates because Jacob also made it a rule that Man in Black could never lie. Man in Black got around this by not always telling the whole truth and by saying things that were true, but that others would take to mean something other than their true meaning.
Why didn't Jacob want him to leave the island? The easy answer is that he was evil and would bring evil into the world instead of keeping it contained on the island, but I'm not sure I buy this answer. It could be that Jacob didn't want Man in Black to spread the word about the island, thereby subjecting the island to people who would want to exploit it. But this reasoning seems flawed, because Jacob could have made a deal or a rule to let Man in Black leave in exchange for him keeping the island secret. I haven't come up with an answer for this one that I like. Do you have a theory?