Thank you! I agree about the cooldown timer or similar mechanism. One thing I was thinking was having the enemy have an invincibility timer after being hit where it can't take damage BUT still turns the missiles hostile. It would make the gun upgrades a disadvantage which is what I was originally aiming for.
And yeah, I enjoyed writing the ending. It's kind of a tongue-in-cheek morality tale. Notice how YOU are the last opponent you face.