Zelda more than likely won't be working with Nayru's Love, Farore's Wind, and Din's Fire, as those are the "Good" magic elements that she employs.
Well, Zelda is either surrendered or controlled, right? Not possessed or anything. So she wouldn't really know any new spells as a result of this. And just because the spells bear the goddesses' names doesn't mean that a chaos-controlled Zelda isn't allowed to use them.
The light arrows hit the mirror, and the arrow portion of it shatters against the mirror, leaving only the light aspect to be reflected against Zelda.
There's a continuity break here: I remember the final battle of The Wind Waker, and I recall that a Light Arrow is reflected by the Mirror Shield in its entirety - both physical and magical component.
Think of it like Cave Story. You can fall into that pit to get the Booster, or you can figure out a way to not even have to, and get the booster 2.0 later.
Also like Cave Story: there should be no saving after the battle. If there's two endings, we don't want the player stuck on the "wrong" one.
Which reminds me, here's another idea I have to bring forward. It's about the two endings. I think it'd be interesting if each ending to the Zelda battle led to different endings of the entire game, rather than one ending leading to Game Over.
This post contains an idea that I like: the opening of NeoFirst begins with an unseen narrator telling how their friend saved the world. And, at the end of NeoFirst, the narrator finishes the story.
• Here's one way it could end: If you slay Zelda, you get to take her corrupt Triforce of Wisdom and unite the corrupt Triforce. However, when you defeat Menace's first form, Zelda's ghost appears instead of King Dim's, and she tells Link that it's too late to save the Triforce, and he should stop fighting Menace, because it is still impossible to destroy him. However, she says that just as the Triforce-powered Golden Arrow can temporarily open portals in the Temple of Shadow, so too can it temporarily close portals in the Temple of Light. What's more, the complete Triforce is powerful enough to destroy the portals entirely. So, Link can run away and use what little is left of the complete Triforce's power to destroy all of the portals at the Temple of Shadow, thus sealing Menace in the Sacred Realm. [Or something. This may need working out.]
So instead of fighting Lord Menace's second form, there's an old-fashioned escape sequence back to the Temple, whereupon Link is forced to go back through all of the light/dark warps once each, destroying them as he goes. Maybe the last one has a surprise custom miniboss of some sort in front of it, just to round things off.
Then we get the ending sequence, and the book, and the unseen narrator laments that this is not the optimal ending: the complete Triforce can now never be unsealed, Zelda is dead, and with her the royal line of Hyrule is extinguished. The narrator says, though, that most importantly "she was my friend... and because of her, the entire world has survived." It thus becomes evident that the "friend who saved the world" mentioned in the introduction is Zelda, and the narrator is Link himself.
• However, in the best ending (which we have already discussed) the narrator is Zelda, who talks about how, with the power and guidance of the complete Triforce, she has driven the monsters from Hyrule and returned to her rightful place in the Castle - and that Hyrule is slowly being restored to the glory of her grandmother's age. "But had it not been for my friend ... I would never have returned from those depths of chaos and despair* - nor have ever forgiven my father."
Thus the story literally becomes the "Legend of Zelda".
*Word choice may vary.
EDIT: Added to the Plot Tracker topic.