Layer Suggesions

This would make under-over bridges much easier to make. Also it frees you from warps and extra Dmaps and screens.

-0 1 2 3 4 5 6 *
N A B C D E F P

Layer C is the default layer for ground-level sprites.
Layer E is the default layer for "flying" sprites.
Layer * is a variable layer that can be set to a layer from scripts and it may also be changed by flags. By default it is on layer C.
You can change which layer a ground-sprite is on with flags and scripts.

To go along with this, I propose a few Quest rules:
Flying enemies can change layers at will
Flying enemies only hurt link when on same layer

Also, another feature - layer walkability
It defines your walkability when the tile is either below or above the sprite. Generally, you want the Above one entirely walkable.

-XX-----XX
-XX-----XX
Below--Above

And finally, edge flags. You can set each tile height/width segment to one of the following:

A B C D E F N P R

By default, C is the edge flag of each segment.
Obviously, A-F and N and P set you to that layer when entering from that segment.
And R means retain. Basically it just doesn't reset the layer to C, therefore carrying the layer data over.