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I believe that season five has left us several hints that John Locke is actually Jacob.
1. John 3:16 Let's first make two assumptions (which are by no means definite but certainly probable). First, let's assume that Jacob is a benevolent god of some sort. Second, let's assume that the number 316 that has appeared so many times is a reference to John 3:16. Notice that Jack receives Locke's suicide note but does not open it until he is on flight 316. Locke's note succinctly states, "I wish you had believed me." If we look at John 3:16 it says, "For God so loved the world that he gave his one and only Son, that whoever believes in him shall not perish but have eternal life." In Locke's note, the person to believe is John Locke. In the Bible verse, the person to believe in is God. Since Jacob is a God-like figure, it follows that this is a reference to John Locke actually being Jacob.
2. "Hugo" Throughout the series, only three on island people address Hurley as Hugo with regularity: Sawyer, Ben, and Locke. Over the last couple of seasons the only character that never refers to Hurley as Hugo is John Locke. Not only that, but John Locke is actually the first on island person in the show to address Hurley as Hugo. He also starts consistently addressing him as Hugo all the way back in season two. In the season five finale, Jacob and Hurley have a conversation with each other. Jacob addresses Hurley three times, each time referring to him as Hugo. If you listen to the way Jacob speaks in their conversation, it is similar to the way John Locke speaks in previous conversations with Hurley.
I think it is important to note that just because a different spirit is in John Locke's body, that does not mean that John Locke's body can not be in a different spirit.
Please share your thoughts, supporting arguments, and counter arguments.