gbaz69: My deep impression and understanding of this game is that it is extremely luck based.
I seriously doubt you can beat the end boss with multiple strategys, that work for every other encounter cept last boss.
Last Boss strategys that don't work:
1. ship bording
(every battle up to this point all you had to do was beem over and go room to room, but the end boss has segmented sections, negating this tactic)
Actually the fact that the ship is segmented
helps this tactic. You only need 2 decent boarders (preferably with a level 3 teleporter) to take out all 4 conventional weapons systems in the first boss battle, and then those stations are even easier in the second and third battles since you've killed off those crew members. I usually hit missiles first, then ion, then their laser-type, then the beam. After that it's just a matter of getting through the shields to do hull damage.
gbaz69: 2. any all non-missle weapon load out...
(even with the best possible lasers focus firing on one section will not win this battle, cause bosses shield restore rate is insane)
My last win I used glaive beam and ion blast 2. Tearing apart the boss took little effort with that combination. I could have activated my crystal burst weapon as well, but decided to put the power into engines instead. Most of the time I don't use missiles at all. It just depends what the game gives me, and what my ship is.
There are many different ways. A favorite of mine with the rock B is to fire bomb his shield room, then teleport rock boarders into it. They can't fight the fire; fire spreads; soon there's no shields and you can take the boss out with a pea shooter.
You just need to learn more about the game.