I might be covering a few already mentioned but these are things that would get my 3Derizing more games.
+ Object voxel painting. Voxel per voxel manual painting for objects with weird shapes or suggested foreground parts of sprites so we can make it stand out and paint behind it where it covers up supposed parts of the sprite that could otherwise not be seen.
+ Sprite/Object recoloring and replacing for fancy full color repaints. (Though palette changes might cause a bit of trouble)
+ Precise Z location placing (I figure that would happen soon anyway)
+ Smart Z location movement based on position of sprites under it. (rarely needed but might be helpful in odd games)
+ Camera scripting.
For things like placing the camera behind the player sprite, attempted third person views, camera tilting based on button presses or sprite/object location. Maybe even zooming or other functions based on memory values like used in cheat codes
+ Object naming, listing in an easy to edit text window. Also a notes and comments section.
Maybe some aren't all that needed up but I'd overall just like more control over things and quick ways to edit and document things for handing over 3dns file projects others and more difficult games.
Plus some extra features just to further enhance things would always be great.