Congratulations to all you hard-core winners!
I'm not quite there yet unfortunately, but soon...
AdamR: Congrats!
I'm still working at it. I've only made it to the boss once (using the Red-Tail.) I was thrown off by the flagship's slightly altered layout on hard mode, which resulted in my swift and brutal destruction.
Same thing happened to me as well! The thing is, this was my first hard run and I must have lucked out because it was pretty easy going - was using the Kestrel A, managed to get decent crew and equipment (just had stuff handed to me basically, so had drones and cloaking reasonably early). So the fights leading up to the flagship weren't overall harder than usual, though there were a few fights where it took a while to actually win the fight (which was no issue since in those they couldn't do much to me).
Then I get to the Flagship and I didn't even register that it was different - I just attacked it as per usual, teleporting into the missile system first without even thinking. By the time I realised that the enemy crew were swapping out and healing and that it was connected to the rest of the ship, I was pretty well gone.
My second run ended up with me getting whooped before the fifth sector, and to get there I had to spend way too much scrap on repairs, so my ship sucked by then.
I'm so glad they added this mode to the game, should increase the longevity a fair bit if this keeps up! ;)