Hi,
I think that depends on your resources and style you want to give your game.
I think making that with 2D nodes will require a lot more work, because you need to create images for all directions and also top-down additionally.
With 3D nodes you just create models and you can render from any direction, so don't need to create as many assets (for me that would be definitely easier, since I draw really slowly before I create something looking good enough).
But I think final decision is up to you. That depends on effect you want to achieve, because of course 3D version will look differently than 2D.