Actually, that does make some sense :)   Hypothetically, if the Empyrean enemy ships were separated into specific classes, that would differentiate them from mere Grineer. You're basically shooting the vehicle rather than the pilot themselves, so I think that could be a fair explanation for changing how they're taking hits.  Thinking back to Starfox Assault, Arwings can have their individual wings, etc. shot at, damaged and blown off (Multiplayer / certain missions would be a grea