Figuring out how to beat the final boss and beating it for the first time was very fun.
First few runs I got confused on the final boss map, ended up going to rebel controlled territory, escaping into final boss with a extremely unprepared / damaged ship.
I ended up having to unlock several more powerful ships and beat it via the starter Mantis ship (no weapons starting off + 2 mantises). On my first successful run, I had a double charge II laser, a lvl3 defense II drone, and a 4 man warp pad, so the final boss ended up being pretty easy with solid focus fire damage, boarding, and defense.