Thank you for the review! I actually just added a pause menu to the game last night as well as added controller support to the puzzles. (I haven't uploaded an update yet. :D)
Thank you for describing your problem with the puzzle. I'll try and think of a way to make it clearer or to make the hint clearer.
Thank you also for the feedback on the movement, I'm still trying to figure out all the pros and cons of the different configuration options. I'll focus more on that in my prototype 3.