Its a feature request at best.
As in
Ashley can I have layers with separate width and height scale?
Scale is somewhat complicated already changing just the height makes it harder.
10x10 /2 = 5x5,10x5 /2 = 5x2.5
Then apply that to a matrix....
Edit:
Also you would want it as just for layers, as you would want regular layers for gui, etc.
But that makes it even more complicated, as you would have to keep track of the layout to layer xy's for each layer.
Sorry but the strange isometric calculations are the best way.
This is one of the better explanations:
http://clintbellanger.net/articles/isometric_math/