Well, it depends on whether you are going to do a free public personal project or something serious and commercial.
You could use Unity but that brings piracy and performance problems, a good option is Octave or creating your own "engine" for your game (That's what I did with devkitpro and C++, creating the "engine" for RAI Loader)
Unfortunately Godot for 3DS still has a long way to go to be usable.