It is really well designed! Different firing modes, bombs, enemy behaviours - all of this feels like a necessary addition rather than randomly glued mechanic. The tutorials are another strong part - seamlessly incorporated into the levels and straightforward which is very important for this kind of game.
I have also struggled with incorporating the theme into my game, it's easier said than done but I suppose if there is a weaker side to the submission that would be it, since at the end I wasn't sure if I have run into a bug or if being locked in a room after the fight was intended.
All in all - I think you have done an amazing job here with the game mechanics!