Here are a few suggestions of mine:
First of all, in Zquest, an option of scrolling the screen in any direction. This would be useful if say you wanted to make a series of animations. What would happen is that you would pull the screen in any direction, thus you could adjust it to your specifications.
The second thing is the idea of having layers follow certain monsters. For example, let's say that I want to have a death knight that instead looks more like a tank. With this, I would make the tank graphics, and then select at what point the enemy would drag the graphics arround(in this case it would be in the centre, like he's driving the tank). The layer would follow the sprite arround, untill it dies, in which case it would disappear. It could even be programmed to deal damage, which could allow for things like spiked log rolling traps, and stuff like that.
Another idea would be a tile that when push against, would automaticall sent link up a pixel, sort of like having curved edges in the game. It would work better with diagonal control, but it could be used as is for some effects.
One more idea is the ever so classic warp that is activated by pressing the A or B buttons. This would make using side warps in cutscenes obsolete. What could be even better is a combo that warps you differently depending on what button you press. For example, a yes or no question that determines your actions. If the anser is yes, you press the A button. If not, you press B. Under the Warps section, a side warp could be assigned to one button, while another could be assigned to the other button. The tile warp could still be used as well.
I heard a suggestion about splitting the screen into 4 sections, each quadrent leading to a different area. This might not work exactly, but the simplist thing is just that warps should just be overhauled.
Instead of tile warps, side warps, ect, what there will be is a list of about 10 warps. You select things as normal, but there would be an extra field, which is what kind of warp it will be. Under the menu would be several options: Stairs warp. direct warp, timed warp, timed direct warp. In the combo screen there could be an extra parimetar that would be from 1 to 10. This would work for whatever combo you selected. Right now, for stairs and direct warps, 1 to 10 would indicate what warp it would use, and you could have from 1 to 10 different warps on the screen at a time, with what warp being saved directly into the combo. Other combos could make use of this, perhaps a 1 to 10 for which weapon would break a certain solid combo, or how many hearts a spike tile could do as damage, or even what out of 10 seperate locked door fags would be triggered. This brings me into another idea:
Locks overhaul. Each room would have 10 locks(more than enough, but it fits in with the 1 to 10 idea with the warps), and lock block combos would be renamed lock combos. Basically, lock combos would replace regular locks(although the origional would be available for use). You have 10 locks per screen, and if you unlock one lock of one number, all of them are unlocked. Also, if you somehow appear on a lock combo, either by scrolling into it from another room, or placed on top of it by a warp, instantly the lock will be triggered without you using a key(in the case of scrolling, it would check if the lock is on a screen, and check to see if Link will collide with it. Somthing like this exists in the Oracle games).
Anyway, all of this is very hard work, and what about the Classic Zelda? Well the best idea I can think of, is to have 2 modes of editing. The first would be normal standard Zelda, and the second one would be with all the extras. You can upgrade quests, but you cannot downgrade quests. Both quests can be played on the ZC player. This way you can make a classic quest, and a new nifty quest without the need of worrying about backwards compatablily(since one player can play both types of quests).