The real trick to consistently beating this game is to always horde at least 75 scrap, and buy a Teleporter as soon as possible. Then, buy extra crew members. Preferably, these will be Mantis > Rock > Most Others > Engi & Zoltan. Then, near the start of every battle, fire a single volley to set things on fire / distract crews, and immediately send over your boarding party to begin harassing them. If there are too many, pick on them, or attack things while they try to put out fires. Often, this will cause them to give up on one repair, wasting time while they run around the ship. If they're a small crew, then just roll over them with Mantis / Rock strength. Just make sure you don't attack too much, or you may kill your boarders.
This is doubly effective, as if you kill all of a crew, then you (almost) always get the best reward possible, which often contains bonus equipment, and up to 50% more scrap.
By the end, you'll often have so much money that you'll be capped on energy, and just buying alternate max systems. Also, always destroy rebel ship Medbays, and the Fire Beam and Bio Beam are devastating for this strategy.
Finally, as noted in another person's comment, Teleporter makes the last boss remarkably easy. Just Teleport into each of the weapon rooms and kill the operator (starting with Missiles). Notably, don't kill every crew member, or the Super AI will take over for the final boss and it goes into crazy, Ultra-mode.
This is doubly effective, as if you kill all of a crew, then you (almost) always get the best reward possible, which often contains bonus equipment, and up to 50% more scrap.
By the end, you'll often have so much money that you'll be capped on energy, and just buying alternate max systems. Also, always destroy rebel ship Medbays, and the Fire Beam and Bio Beam are devastating for this strategy.
Finally, as noted in another person's comment, Teleporter makes the last boss remarkably easy. Just Teleport into each of the weapon rooms and kill the operator (starting with Missiles). Notably, don't kill every crew member, or the Super AI will take over for the final boss and it goes into crazy, Ultra-mode.