So I played the game, no controller
The first thing is that there should be some kind of indication at the very beginning that you should click on the text to continue, maybe lightly flashing text (I know it changes color when you click on top of it) or an arrow. Whichever visual indication you prefer
The second thing is that when I found the ship, I got to the inventory and used the power cells, but I couldn't figure out how to get on the ship. I saved, reloaded and voilá I was flying inside the ship
It might also be nice to add some minimal acceleration to the ship just for effect