I hope you can reach that vision. It is very cool to hear that your idea is to make this a general tool for any type of 2D game/console. That will be amazing to see! I don't know if you are familiar with programs like Sprite Lamp, or SpriteIlluminator, but they are used to create normal maps for 2D sprite based games. Where those just allow better 3D lighting of 2D sprites, 3DNes gives real depth to the them allowing you to move around them. Its awesome!
Anyways, when I mentioned the sphere shape, I forgot to say that the cylinder shapes make good spheres themselves, but the problem is that they can appear hollow when viewed at different angles. If there was an option to have a filled cylinder instead, that might cover the need to have a sphere shape.
My only concern with the emulator functions coming second is that it can make editing 3D difficult. You need to be more than just good at playing a game. You need to be good at playing a game while editing it as well. Some people just want to play, so making it easier for others to create premade .3dn files for players to use will only benefit 3DNes in the long run. Common emulator functions like save states, or recording and playback could help with that.
You are probably right about the Mario cloud thing. I have no idea what an NES does at a technical level. ;)
Now I have to create an account somewhere to host the .3dn files I have been working on. Any suggestions? I'm pretty new to this.