The Containers make it easier to manage the isometric assets.
Like every tick isobjectA setposition to 2dobjectA.
No picking if the iso object is in a container with the 2d one.
Also 3d would solve the issue with a lot of frames.
Another solution to that could be Spriter animations.
Other than that I don't see much point for 3d, unless you are sure you will have webgl.