The game was a challenge when there was two spaceships, and impossible when there was three. It just asks too much from the player in terms of coordination (there is after all a human limit), and it's such a simple idea and execution you'd have to change the idea to improve it.
I suggest not introducing a second key, having one key cycle through all the spaceships (though the third spaceship wreaks the idea fundamentally, this might help a little). Or if it was touch screen based you could select the spot between spaceships to swap rather than using a specific key, that could help too.