Well I've beaten it 3 times now, played it for over 50 hours, and I still see no end in sight. I guess I'd like to unlock all the other ships, I only have 4 unlocked so far, so I still have 5 to go (that's not including all the B types, of which I only have 2 so far). It seems a little insane that I have so few after 50 hours, but I seem to have extremely bad luck. It seems when I run into the right scenario to unlock an alien ship, I always make the wrong damn choice.
To give an example, I ran into (what I think was) the Zoltan Ship Quest, and the situation was something like this:
You see a fierce battle between the mysterious Zoltan and a powerful Rebel ship, do you:
1. Make first contact with the mysterious alien race.
2. Attack the Rebels in defense of the alien ship.
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Well I chose option 1, thinking "first contact" would mean some form of communication between us, but actually "first contact" apparently meant "blow their ship up"; which the text was very unclear about. So instead of saving them, I had to fight them, and then got nothing for it in the end. Needless to say I was a little frustrated with the ambiguity of the whole situation and my own crappy luck.