There's 3 basic tips I'd give for the game in general.
- Evasion is king. You want max engines, and a 2 star pilot and engineer by the time you get to the boss. The 4th shield bar is largely unnecessary in comparison.
- Bombs are the best weapon type. They completely ignore shields and defense drones, breaking or disabling systems, as well as damaging crews trying to repair them. If shields are an issue, bombs are your answer. Maybe pass on fire bombs, though. They're slower, and less reliable.
- Boarding is extremely effective, as long as you're careful not to accidentally kill your own boarders by blowing up the ship they're on (looking at you, Osprey artillery beam), you'll get way more rewards for your victories, and often bypass extremely difficult encounters with heavily armed ships that have very small crews.
I wouldn't say beams are bad weapons either. It's easy to get into a situation with lasers and ion weapons where you can barely take down enemy shields, but do 0-1 damage to the actual ship. Beams turn that 0-1 damage opportunity into a 6+ damage murder beam that'll wipe out the boss before he even has time to do anything to you.