I like Screen->Secrets(false), and I can;t believe that I forgot about this. Really, I'd like to make it possible to individually set/unset screen secrets.
Have you ever used the Age of Kings scenario editor? In particular, the trigger editor? If Zquest could do anything remotely like that, that would streamline an enormous amount of design and script work.

I was actually thinking of doing something different: Making pre-packaged quest templates, for quest styles, that have pre-included and compiled items, and engine effects. I've already been working on one that emulates the Gameboy style games, and we could include things like that to allow expandeditem lists, without needing to hardcode them.
This sounds FANTASTIC. Would love to hear more/update status.

For my own needs:
More utility in using secrets/flags.
Talking NPCs hardcoded.
FFC's movement behavior that can be manipulated by secrets.
In sum: the ability to make a basic cutscene without using scripts, with NPCs having a conversation, moving around, and performing actions.
I think these have been requested already, just adding them as my own wishlist:
Sideview ladders
Enemy type editor
Map sizes increased (16x16?)
View menu: Ability to set palette per map in addition to per screen.
Subscreen editor: ability to place/move elements with a mouse.
Pie-in-the-sky, prolly 3.0 feature instead: all layers compounded into a single map screen, with a toggle to work on different layers.