I understand that the content of the last dungeon hasn't been decided. I also know that part of NeoFirst quest's plot involves the creation of a dark world by the extraplanar entity, Lord Menace*. So, here's my proposal: The last dungeon will in fact be an entire "dark overworld".
Now, this'll be quite different to Zelda 3's dark overworld. Its colour scheme won't be dim golden-brown. The music will still be "Ophidian". There won't be any accessible buildings, dungeon entrances and such. There will be the standard dungeon tropes - treasure chests, locked gates, minibosses, the compass and such. It will simply be a "dungeon" that's outdoors and whose design mimics the overworld map.
And, it will have a gimmick - a full-fledged** NPC helper character, in the vein of Wind Waker's sages.
Let me explain further. I mentioned in a previous topic that I'd like Zelda to serve as the quest leader for NeoFirst. Now, the reason Zelda knows about the corrupted Triforce in the beginning is because the taint is displayed on the Triforce of Wisdom, which she has in her castle (or sanctuary or villa). After you get the Triforce of Power from the place where stone flows like water, both Zelda and Wisdom are conspicuously absent. (Yeah, I know, but if NeoFirst was afraid of cliché we wouldn't have either of the first two dungeons.) After some overworld busywork involving the Temple of Light's ruins, you meet Zelda at the start of the last dungeon and together proceed to get the Triforce of Wisdom back.
There won't be any Command Melody to seize play control of her, and you won't be able to give orders ("c'mon" etc.) but she'll have a minor degree of autonomy - moving onto vital switches, opening "secret" doors and possibly using magical attacks on enemies (Nayru's Love SSBM?). It's definitely possible (albeit laborious), and I think it'd be something that many quest makers would like to see an example of.
* What better name for the Enemy of NeoFirst's world than a combination of the screen names of the two authors of First Quest?
** "having the feathers, fit to fly." - Etymonline.com
