Yeah, the throwing controls do need a tutorial and feedback. Something like a power bar, or at least an arrow would help a lot.
The stuck ship is a bug (unfortunately very well known, many people have encountered it :( ).
The lack of control was a design decision. There is actually a lot you can do to influence the outcome. Trowing a correct unit to a correct spot does make a difference. But it definitely should be more obvious.
I'm very happy to hear that you enjoyed the game. Thank you for the feedback, I will address all of these issues after the judging period ends :)