Using 2D as a representation of 3D world.
I mean the level is made in 3D so you still can use the collision/physics/movement/anything you like in the 3D engine, but don't show it to the screen(reset camera.SHOW).
Now get the x,y position from the entities in the level, and use them to put the 2d sprites on screen. You can use some equation to convert the position to isometric coordinates(should be easy).