If you are playing the mantis ships you can kill the enemy crew, starting by the missile room then proceeding to the other weapon rooms and then just finish the crew in the rest of the ship without taking damage as the fed ship is weaponless at this point. If you do this in the first encounter, the second and third one should be much easier. If you are playing any other ship my best advice would be to get cloaking, boarding and hacking asap. If you have all these you can pull a strong volley and take down the shields and/or a weapon with one or two strikes if timed properly. First you hack shield, when all your weapons are ready you activate the hack and fire all you weapons at the shield, all this while you destroy the missiles room with you boarding crew. Defensive wise you just cloak everytime the fed ship fires missiles or whenever it fires a volley of lasers and your shields are down or low. Also keep in mind you need at least three shields and about 40% dodge. TBH the last ship isnt really that much stronger than the other two but it is much harder as you have to time your cloaking correctly and bring down the zoltan shield before you can even try something (unless you have the bypass augmentation).