Ok, so my theory is similar to one on the Jacob Theories page, but not exactly. That one states that Jacob is Richard Alpert from the future and he uses his future self to direct the others while still appearing as an advisor.
Mine is similar, but also connects to why Richard doesn't age. Here goes. . .
Jacob is like the portrait of Dorian Grey, except more. . . interactive. If you are unfamiliar with the story, its about a man who's portrait becomes aged and disfigured, while his physical body retains its youth and beauty. But if he ever looked upon the painting, he would age rapidly to catch up with time (and effectively decay and die, as it had been many many years) and the portrait would portray his youth.
So Richard Alpert ceases to age and adapts to each new era while Jacob, as Alpert's true age, is confined to the cabin (portrait) and retains his older personality and dislike for technology (because it is not of his time and can't accept it maybe?).
Hence, my guess is that Richard will refuse to have anything to do with Jacob once they get there, and if he finds out Locke's plan, he will attempt to stop John.
That's all I have to say.