It was mostly just for the lack of documentation, I think I've got it mostly figured out now. Things I didn't understand were, for example, what the job of a science officer or security was, exactly, or what the different unique planet features meant (which for that one, I now see is intentional so the player can figure it out).
I also didn't know that weapons and cargo bays used the same slots, or that buying a better ship hull would give you more of both, but everything can be learned without too much trouble by experimentation. Basically the readme could just use a bit more expanding rather than any changes to the game itself being necessary.
While I'm at it, another thing that can make the game more confusing is that whenever something happens, the interface doesn't reflect that until the next turn. So if, for example, one of my security officers is exploring a planet with acid rain and dies, he will show up as alive on my status screen until after my next move.
I actually came pretty close to winning once, having found profitable trade routes and the best goods to sell between them, but unfortunately the space pirates also took an interest in my business.
Most of the time I've been trying to play an explorer, but money is definitely harder to come by that way than it is through playing a merchant. My favorite death was when I came across an alien who demanded that I worship him.
Overall I think you've definitely got an enjoyable game on your hands. I'll be sure to follow your progress with it.
Edit: Alright, I've had a winning run through the game now. I wanted to win by doing something cooler than working as a merchant, but after two bloody and unsuccessful assaults on the pirates' homeworld I switched to the path of least resistance.