I can actually see his point of view, especially for the day and age he lived in. The views of science had started to peel back the once mystic veneer of the world and reveal that it was "all science, all the way down", but had not yet evolved to the point where they started to realize that there's an entire universe of "still not having any idea what's going on" within the structure of a single atom.
It was as if an author in a novel about an author started to realize that he himself was just a character in a different novel and rebelled against the words on the page, still not yet realizing that there existed another layer beyond them of novel writers. His embrace of the concept of cyclical time and predestination through sheer mathematical elimination of all possibilities was another brilliant but limiting idea that indicates to me a philosopher who has reached the end of his understanding and (through no fault of his own) is unable to make that next leap forward.
My question really is a highly complicated one, so I don't know if anyone else would be able to answer it without being versed in Nietzsche, but here it goes: By going the opposite direction of Nietzsche's predicted path which evetnually leads to his ubermench/superman ideal, does Omnitheism (by Nietzsche's standards) retreat back down the ladder of man's evolution, or does it take an entirely different path he failed to predict, a path that avoids the problems of nihilism while still moving towards the same general direction (the cosmic acceptance of our role and self-empowerment by overcoming our shortcomings) as his ideal?