Engi A, with ion blast II, fire beam, and a heavy laser 1, with system rep. drone and an AP drone. I had 1 Mantis, and 3 Engi (My human crew member was killed by boarders beforehand), so I didn't think boarding was a viable option. Didn't think it was that bad at the time: "I'd beaten the game plenty of times before," I thought. " I've only lost 1 crew member this playthrough, my weapons have been excellent throughout. What's the worst that could happen?"
Oh god it was bad.
https://100001.onl/ https://1921681254.mx/ Basically I would get the flagships shields down to 1 bar, then it would cloak. Rinse and repeat. I had max shields so it couldn't do much to me either, so we sorta waved at each other and exchanged pleasantries for a hour, before I got bored and decided to open all the doors and turn off the shields.
Pro Tip: get something that can get through shields
