More shapes: Agree in general
Custom Shape: Agree in general. But two factors are not mature yet : modde and good technical solution
Z Position, Sprite Groups: Already discussed. It will be supported in the future
Background sprite front faces on same plane : nice observation :) This is due to a historical resolution. When i was testing 3DNes on Castevania, the background was devised into sprites with different depth so i set it that way to have a perfect flat background without the need of any further customization. It concerns only the way of rendering and doesn't relate to 3d data. I admit it's not "correct" way to do in long-term though. I will fix this behavior in future update.
Mario Bush and Cloud: If i'm not wrong, they are seen as different shapes in Super Mario Bros :)
My vision for 3DNes is: this is a generic tool to convert any 2D console game into 3D/2.5D one. With that in mind i will focus in improvement of 3Dification part of 3DNes. The Emulation functions come second. Virtual reality will be integrated. Porting to different platforms. And finally apply this technology to other 2D consoles. I'm open and well-come to any feedback and suggestion to make this technology better.