These other possible suggestions are not quite as critical, and more of a quality of life improvement, if anything. Adding an Undo button would be nice for the 3DNES as a whole, although that might be quite complex, and is not particularly necessary, when you can just do something over again so easily.
However, something fun that could be added (Although it would still likely be difficult) Would be adding lighting effects to objects you have selected. Maybe they could change and cause shadows? Additions like that would certainly add a bit of spice to some games... Although again, it might be rather difficult.