Sorry, but you do realize the 3DS is a 240p screen, right? How would you manage an entire ship on a screen that only manages to be slightly bigger than what the NES showed? 320 x 240 pixels isn't a whole lotta real estate. The idea, interesting as it is, just wouldn't work. You sometimes need fast reflexes, and that swap wouldn't work so great. The vertical split wouldn't do well either as you have to keep a fast track on their ship and yours using subtle visual clues.
This is a console they had to settle for a Minecraft knockoff on, mind you.
Now the Vita on the other hand, not only has the resolution, but also the real estate to make this work on. And enough fine controls. Just a nice split screen would do.