in the first couple of sectors upgrade your shields to 2-3 and when you encounter a ship that cannot puncture your shields let your crew level up by evading and for pilot and engines, regening shields and shoot 1-2 lasers without knocking out their ship for your weapons, it can help give you an edge , it is a little boring however just sitting there lol. Dont forget that you can man your door and sensor systems now for a 1 level boost to the system as long as its manned. it can be handy when you are short on scrap

I've read that some people have luck with boarding early and taking out all but one guy, bringing the boarding party back, then constantly hammering the drone control however possible

I've made it to the end a few times now, but I just can't defeat the flagship the second time. The first is a piece of cake, but once the drones come out, I'm ♥♥♥♥♥♥. I had a REALLY beefed up ship the last time too...*sigh*

some things I've been learning - best to milk the early levels for scrap as much as possible before ships with 2/3 shields start showing up, upgrading blast doors helps a ton, and taking out their crew with a boarding party gives you a lot more scrap, but only do this when you've upgraded your sensors so you can see who's on their ship!