I've only been playing about a week, but I've won a bunch of times, and have unlocked up to the mantis and have the lanius cruiser, with a couple random form B ships, (although I haven't enabled Advanced content yet.)

Personally I don't find engines are that great of an investment; they're not reliable enough. Your pilot is gonna die and your engine room crewman is gonna die. It's a huge investment to get 50% dodge and a couple of bad shots wipes it out.

Cloak is great, but don't buy it too early.

I find with the Kestrel A, shields up to 2 by the end of the first system no matter what is critical. That should hold you for a couple of sectors while you pump everything you have into weapons. (Or up to whatever level you need to run the guns you have then max shields.) The faster you blow something up, the sooner it will stop shooting at you. 3 shields in early sectors will make you invincible, and if something has missiles you can just focus on the weapons systems.

If you can get a hull repair drone, go for it. Or a defense drone, but don't pump too much into side systems without maxed weapons and shields.

All of this matters because of course the more scrap you have saved on repairs is more scrap you can spend on guns.

Try to get a strategy that lets you deal with drones / shields but also does good damage. I've easily beat the flagship with 1 Ion 2 and a couple burst lasers. Focus shields, then weapons / O2 and, keep bouncing back to shields to keep them weak. The faster you crack the hull the sooner it will stop shooting at you.

If you're making to stage 2 of the flagship you can totally do it!