I think right now at least, the endgame is boring. There is nothing to do. I think it would be cool, if like enemy flagships would still surface from time to time, as like cog remnants or something, or maybe an enmy drillship more powerful than a flagship (like a boss), would give you something to fight after beating the game. The boss kind of ships that would be super hard, could have like their own built in power areas, to explain how the cog survive on them.
Making this a general post.
^ This one is more about map exploration after beating the game.
^This one is about changing the lore and making you hunt the remaining COGs after destroying the last laser.