yeah this boils down to decision making. I too ran about 50ish hours before I finally won a run. Once I realized what's the best course of action, I stopped losing runs. Granted you aren't gonna win them all and some runs will have a 4 man invasion overrun your one Engi crew lol. I now have well over 100 hours and I win most of my runs though losing only because I'm just trying to make achievements.

Heres some of the things I do. Always attack ships to gain scrap. Get weapons that wear down shields and their weapons. A one ion disrupting weapon focused on their shield room with a multihit laser focusing their weapon room works wonders. Focus getting scrap to put into getting cloak. Cloak is practically mandatory against the final boss but also useful to use against multi-hit lasers and missiles that ignore shields. Also theres no shame running through on easy mode and not starting with advanced options.