To be fair, Hydaelyn hasn't really done much in the story either - Other than pull some literal Deus Ex Machina moments out and then give you some vauge advice. Like Zodiark she interacts with the world mainy through her minions.
This brings up all kinds of other important questions that we're never going to get answered though. If Zodiark can replace Hydaelyn, does that mean at some point Hydaelyn could replace Zodiark in the future? If so, then we're looking at a universe that is much like a Day/Night cycle and Zodiark rising to power is something that I really shouldn't be concerned about. How do we go about stopping it? If its an inevitable and natural part of the universal lifecycle should we be stopping it anyway?
Once Zodiark is made whole again and has usurped Hydaelyn, then what happens? What does Zodiark intend to gain from it? What do we have to lose from it? Why is he even doing it in the first place? It's strongly implied that there are some worlds that Zodiark has already laid claim to, but for what purpose is still unclear.
Keeping Zodiark, and by extension Hydaelyn, in obscurity as the big bad and the ultimate good in the universe means that we're never going to get answers to these kinds of questions. Moving them both into a position where they are key players in their own conflict would be a solid story move. Unfortunately that means they both need to be better defined, because at the moment they're just sort of... There.