I agree that it is a bit clunky. There are a couple of things that should be done to the designer to make it an easier tool to use. However, I wouldn't say it was unintuitive, but rather that it tries to give you as much freedom in design as possible by giving you a blank slate. This is in fact it's great strength that it gives you this freedom (only constrained by the limitation of parts) to create whatever you want.
However, the game is still lite on explaining how things work. For example: the placement of ship equipment doesn't matter and in no way will impact the performance of the ship. So weapons will fire in all direction regardless of which why you face them.
So I sort of agree on 2 out of 3, which Meat Loaf considers 'aint bad'.