The story isn't about Haruka at all. It's about Yuu deciding who he wants to be.
In the English dub, Tobi's being female takes on an extra layer of meaning since it implies that she, not just Miho, is a Replacement Goldfish for Atori's little sister. Doubly so because Miho and Tobi share the same English voice actor.
Fridge Logic: There are an infinite number of dimensions which are produced from every possibility in every moment in time. Central to the plot is a future event in another dimension which will destroy all dimensions in the multiverse. Shouldn't the universe have already ceased to exist? note To prevent Natter from reaching critical mass, go to the Discussion Page for more detail.
Much of Noein's (the character) atmosphere and aura were betrayed by the way he fought Yuu and Karasu in around episode 20 which involved him performing a Hurricane punch and a Hyakuretsuken.
The English dub would probably be a lot better if two of the main characters weren't named "Ai" and "Yuu." It gets...confusing.
Narm Charm: It makes for some pretty awesome lines, though. "I am you/Yuu", "Because you're Yuu/you", etc.
No Yay: The way Noein treats Haruka in the last few episodes is dripping with this, made even worse because Noein is Yuu, and was legitimately Haruka's true love once upon a time.