"Z-Layering"

Something like this, which establishes tiles on the Z-axis:
http://img527.imageshack.us/img527/439/zlayerkz7.gif
This pretty much explains itself, where tiles can determine what Link can jump from, to, or hit his head on depending where these tiles are on the Z-axis.

Also, to eliminate walkable combo errors, Link and the enemies should have a "Z-Checker" to determine where they are on the Z-axis and what they can walk on. For example, if Link is at 2 on the Z-Axis, he can fall off a ledge onto a layer at 1 or 0.

Automatic additions--
Bridges. Link can now walk under and over(and hit his head on) bridges without triggers or screens.
Ledges. If there is nothing where Link walks to, Link "jumps" off to the layers below.

Other Additions--
Jumping enemies add a number to their Z-Axis while jumping up; they subtract while going down. For example, A Tektite's jump from Z-Axis 0 goes up 3; but it lands on an area with a Z-Axis of 2. It can land here, but from there to a Z-Axis of 6, it can't reach, so it bounces off the side before landing on a reachable area.

"Ascend/Descend" flags will need to added in order to reach different Z-Axises.

I know, there's much more than this, but can definitely be a post-250 idea. I can wait, anyways.