Currently there is no real support for an isometric type of game, so I figure if we want it in the future we better start talking about what features are needed, and what can be done with what we already have.
To start off one feature I think would help out a bunch is a way to configure the grid to make it easier to place tiles. The thing is there are two problems with a grid like this. First off the grid would need two different sets of rows. One row starting at the edge of the layer, then the next offset by half a cell's size.
Secondly the ability to have tiles overlap. I suppose what would be needed is a way to force tiles to snap to grid points at hotspots, or image points.
Next the user would need a way to change the standard 8 directions, to compensate for the change in angles.
Now I realize this stuff can be done already with a few workarounds, Im just saying this stuff would help a lot. Feel free to add any other suggestions.
Also Im sure many of have seen the 3d proof of concept demo posted here many months ago.
Even though this isn't true isometric, I think its worth delving into for this type of game.
Im pretty sure the demo uses 3d boxes, so that means in order to use them there would have to be a few additions to that object, like the ability to find a certain face, and the ability to change textures on the fly, etc.