Once you get some experience, you'll be able to beat the boss most of the time.
More than once, especially in the first two sectors as the torus, you can just use the ion cannon standard with the ship to completely disable their o2 generators and suffocate everyone. Way more scrap early on that way. 
And Rocks are awesome for boarding crews. :3
Anyone care to post their successful strategies?
Upgrading your systems will also help with certain events: Medbay, helm, sensors.
If an enemy boards near an airlock, open it! Once they start suffocating, they will abandon any attacking they are doing to a system in a room and try to force their way out. Level 2 doors can almost hold against one (non mantis) attacker for about as long as it takes to suffocate them, or at least make them less of a threat. Make sure to close your doors again though! Also: Opening doors doesn't instantly vent if the game is paused, and a doubleclick on the open doors button opens all the doors, including airlocks.
If you do have a teleporter for the final boss, the fight is made a LOT easier if you teleport to the missile weapon system, second from the right. There is only one defender and it can't be repaired after you teleport away. You can do this with the other weapons too, but the missile one is the heavy hitter, since it fires 3 and bypasses shields. D=
The final boss is terrible and I have only beaten it if I get cloak. I've gotten close with a boarding party ship, but an AI takes over if you kill all the crewmembers and it autorepairs everrrrythiiing; even in subsequent fights. I wonder if leaving one guy alive will mean the other phases will only have one guy also.
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nem-x attempted to be funny by writing:
I wonder if leaving one guy alive will mean the other phases will only have one guy also.
Yes.
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nem-x had this to say about Jimmy Carter:
I think the biggest thing that improved my gameplay was to stay in each zone for as long as possible before hopping to the next one. Rushing Shield 2 helps a lot also. I keep autofire on and just press the weapon number and then right click to deselect when I want to sync shots if necessary. I like shoving surplus scrap into helm/o2 and the other subsystems so that they don't go red if they happen take one point of damage. Scanners aren't really necessary unless you plan on killing crew.The final boss is terrible and I have only beaten it if I get cloak. I've gotten close with a boarding party ship, but an AI takes over if you kill all the crewmembers and it autorepairs everrrrythiiing; even in subsequent fights. I wonder if leaving one guy alive will mean the other phases will only have one guy also.
Yeah, if you manage to kill the crew in the weapon compartments (The center two, at least) they don't come back. The ship has a lot of crew, though. And I will second staying in the zones as long as possible. Try to plan out your routes. You get a feel for when the dots will "connect". A few times I thought a path would connect to the exit, only to not do so on the final jump, causing me to backtrack through about six sectors of rebel fleet.. yeah, I didn't survive that run. 
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Delphi Aegis had this to say about Optimus Prime:
Yeah, if you manage to kill the crew in the weapon compartments (The center two, at least) they don't come back. The ship has a lot of crew, though. And I will second staying in the zones as long as possible. Try to plan out your routes. You get a feel for when the dots will "connect". A few times I thought a path would connect to the exit, only to not do so on the final jump, causing me to backtrack through about six sectors of rebel fleet.. yeah, I didn't survive that run.
Go to the options menu. There you can activate a preview of all routes on mouseover.
