This is a really interesting question to consider, and I would be tempted to answer it by thinking about the way in which Ishmael as a character represents something of a contradiction in the novel as a whole. Let us remember that Ishmael is above all a character who is profoundly intelligent and capable in many different areas. He also claims, in spite of his relating being aboard a whaler to committing suicide, that the whaling ship has been "Yale College" and "Harvard" to him.
However, infamously, this novel is very philosophically rich and complicated. This results in a conflict that goes to the very core of Ishmael's character. Such profundity is set against the backdrop of a world that is occupied by working-class and uneducated men. Ishmael finds himself alone in this world, and left to his own philosophical reflections. Thus the biggest conflict that Ishmael faces seems to be a result of how he is used by Melville. To tell such an extraordinarily rich tale, you need to have an appropriately intelligent and sensitive individual, but at the same time this makes Ishmael stand out from his setting and presents him as being nothing more than an instrument of the author. The way in which Ishmael disappears from the narrative seems to suggest that even he is not sufficient to tell the tale as Melville would like.