I've actually just got past this mission, sort of.
I completed the three Marauder base sub-missions, then on about my sixth attempt at taking out the carrier, I skipped the video intro, and Hoffer congratulated me, said I would be rewarded, and would I like to mop up the remaining Marauder ships (6) which I duly did.
I'm not complaining, and being a bit of a gaming wimp, I was beginning to wonder if I ever would complete the last part of the mission, which takes about 20 minutes to get to, but I would like to have a few more tries. Can anybody give me some suitable combat tips for taking out the Carrier and surviving the mission.
So far, my tactics run like this: I engage some serious sideways thrust, fire off my remaining dogfighting missiles at anything and everything, try and hit the Carrier with a disruptor missile or two, if possible do the same to any cruisers I see, then make my way towards the back of the Carrier for some neutron romance, as per the faq, in practice though, I never get near enough to the Carrier to do it any serious damage.
Any thoughts?
Ravenger? :)

I wrote that mission so you can blame me both for the difficulty and the cutscene skipping glitch!
However it's been a long, long, time since I played that mission so I can't really remember the best tactics. Sorry :(

This time playing through, I've almost killed the carrier several times. ;) Those stupid cruisers keep taking me out, though.
Set your wingmen to defend (hotkey 4) the Pegasus since losing that ship ends in a mission failure.
What's gotten me closest is to try to get behind the thing and hit the weak spot. Once back there, I keep D pressed for sideways movement and twist the stick left (more comfy than twisting right) so that the sideways thrust translates into a rotational movement to help avoid fire while keeping the carrier in my sights. The problem I've had is coming in too fast with forward thrust, so their return fire starts to hit my ship as the ship drifts closer. It looks like the carrier is only moving at around 150-200 so keep your forward thrust low to avoid getting too close.
I may try loading up the turret fighters with cannons instead of Heavy PBCs, so the damage doesn't suffer with range, and try to stay at around 7-8km. I don't activate the turret fighters in the three early base encounters since those are easy to accomplish without losing any wingmen, so Lori and Az should have a full load of ammo for that encounter with the carrier.
My kingdom for a single mid-mission save, a la Operation Flashpoint, just so I don't have to repeat the earlier base-busting portion of the mission every darn time.

Update after blowing it the hell up. Changed a couple minor things:
- As mentioned, I keep the turret fighters silent (F7) during the first portion of the mission, to save their ammo. You don't really need to use them at all to take out the three bases. At the end of the last segment, when Hoffer gives you the 'woohoo' message for taking out last of the Marauder bases, press F9 to set Lori and Az at "fire at will". Make sure that no retreating enemy ships are in range else the girls will fire off a bunch of missiles. On one run through with this new tactic, during the cut-scene with Maas they actually took out a Marauder corvette with missiles before the fight even began (there was a ship-busting explosion during the conversation).
- Instead of F8 to have the girls target the carrier, I use F9 so they will fight off the interceptors that harass me as I go for the big ships. They'll target the carrier periodically if it's the closest enemy vessel within their arc.
- Let your wingmen do whatever they want. If you put enough pressure on the carrier then Hoffer (Pegasus) will do fine on his own since the carrier and cruisers will put their attention mostly toward you.
- Continue to use D or A for sideways thrust. I guess I didn't use it continuously, but did use it for at least half the time anyway, and was twisting the stick quite a bit to throw off their aim. I set the throttle for around 150 and then used W and S to change the distance as needed. For those of you who fly well without flight assist, this may work out even better. Or worse. I dunno, since I just leave it on. When your hull gets down to 50%, jet away for a few seconds and then rejoin the fight. This is plenty of time for your shields to get back to full and for your hull to be repaired. Using my tactics I wasn't being damaged by the big ships - it was mostly fighters and interceptors denting the hull from behind. Jetting away for a moment lets you clear your "six o'clock".
- Most of the fight I was able to stay safely within the 5-8km range. This keeps your shots easily on target and gives the PBCs some punch, while your constant maneuvering will keep your ship safe; get to around 3km and the big ships start to land big hits on you. I was tempted to set full power to weapons but remembered that maneuverability suffers really badly, not to mention low shield power.
If anyone needs help with the earlier parts of the mission (the three bases), just let me know.