Yeah, I just thought about the fact that you can't change the boarding AI. So it's either always invasion or sabotage. If it was invasion without the AI event they just do what they do anyway and board you. Leaving Mr. laser all by his lonesome usually. And if you changed it to sabotage then the entire crew would voluntarily suffocate, lol. I wish you could change the boarding AI with an event.
So on that note, you might even be able to say in the text that the crew abandons ship, only a couple brave souls stay behind to manually activate the AI takeover protocols. Or something...
I thought being able to delay the Rebel fleet for 2-3 turns was a really good incentive to keep mine launchers around, despite a high ammo cost. But maybe because most people wouldnt have that many missiles stockpiled the first time it should be just 5 missiles and a 2 turn delay. You could even say that it will take approximately 2-3 jumps for the rebel fleet to navigate the minefield. That was just my idea though. Making the minefield cost less missiles is another good alternative for a 1 turn delay though. I just thought it was weird having a minefield with 2 or 3 mines, but I guess not everything in this game makes sense does it...
Well the custom backgrounds idea was worth a shot...

Would love to see the mantis fleet in one of the backgrounds at some point.
Lastly, the flagship still uses augments on the third state right? Maybe you should just give it a random possibility of hacking your systems in every stage...