No FTL is not perfect. The final boss fight invalidates a lot strategies that you are encouraged to use throughout the game. Why does the ship continue to function without its crew? I want my pacifistic engineers to sap the energy out of the enemy's life support system with energy weapons until the crew suffocates to deaths. I want my cloned mantis boarders to kill everyone. I want to use fire. But you can't. The only viable strategy is to destroy the ship using regular weapons.