Although to be honest, this turns out to be pretty damn unviable. Okay I'd do this: add an option to flip the bottom screen from double resolution to normal, and make a virtual console for button controls so it's still passable with regular 3DS games. Make it thick like a WiiU handle. The super tiny screen is quaint, like GBA Micro, but it's workable for normal human eyes since 240p is still 240p in any pixel size, I should know because I hated 3DS XL for that.
If there's any hope left for even more features, I'd add hardware for improved download play options that can be worked to stream into Switch and also do something compeltely new with Monster Hunter or something.
Then this could still be entirely impossible if Nintendo has no system to differentiate firmware updates to correct line of consoles without breaking their OS.