Coding it into the game as an object separated from the system , is easy; I just copied the main control codes from the first ship. But what's really hard, is actually to include it into the game system, especially enemies and bullets behavior; a lot needs to be updated, like first checking what game mode it is, arcade or story, and then check if there is 2 ships or just one, and if it's just one, check which of the two. All this before doing anything.
It's mainly my fault that it's such a hassle, because, even if I planed it, I totally forgot about a 2nd ship when I was working on the game.
Update on the 2nd ship: Sub weapons!
https://www.youtube.com/watch?v=X2hEHOIYje4