flagship doesn't even actually have that much evasion, i hacked it to do basically the same thing on stage 1 and it was either 15 or 25 (im guessing 25 when piloted and 15 when not?)
it's just that i didn't have a way to not die from the drone swarm and couldn't kill anything fast enough to actually make a difference despite most of my ship upgrades being awesome
Chloroform girl, how have you been?
Don't let me catch you sleeping again
You're only alive because I like you
It's been three years since you've seen the sunlight
But I know you're having fun
Bound, gagged and chained up in my basement
Also, killing all the crew on the flagship doesn't win you the fight like it does other ships, but it does make the third phase way easier 'cause there's no boarding party. Pro-tip for phase three: Have all your crew in separate rooms so they don't cause too much trouble when mind controlled. That, or hack the mind control system or use your own mind control to counter it. After all, the enemy getting control of a full-leveled fighting Mantis with the mind control buff is not a situation you want to be in. Trust me.
Chloroform girl, how have you been?
Don't let me catch you sleeping again
You're only alive because I like you
It's been three years since you've seen the sunlight
But I know you're having fun
Bound, gagged and chained up in my basement
Upgrade the stuff so you don't take damage first. Like shields. And engines.
Also, in section 6/7 you don't want to repair all the way to full. You're going to get repaired at the start of the last sector, so it's pointless having 30 hull. Actually, the only time you ever want to upgrade to full is maybe just before the scrap per repair point goes up.
Actually, you don't need to repair much at all. There's only one point of hull that matters - the difference between 0 and 1. Besides that, it doesn't matter whether you have 30 or just 3.
My first upgrades are always shields and engines. The more you dodge and absorb things, the more scrap you'll have later to buy those shiny systems and weapons upgrades that LOOK SO COOL RIGHT NOW.
Also, if you ever get in a situation where a ship can damage your shields but not hurt you, you can let the game run for like 30 minutes while you do something else and come back with mad piloting / engines / shield crew skills.