Actually I generally do not put any sort of defenses on my carriers. I generally put in as many extra cargo bays as I can to hold extra fighters. Then I rely on PD cruisers and my other support ships to do my dirty work.
I also split my fighters into three Groups:
CAP (fighters with limited engines but plenty of close in anti fighter firepower to ward off any guys who get through my PC)
Escort Fighters (a decent amount of engines and a mix of anti fighter and anti-ship weopns)
Bombers (Middle range of engines and no anti fighter weopons, just hopped up on missile pods).
I then stick the CAP between my PD cruiers and carrier and launch the remaining sets to go get my enemies.
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Sarge is coming...
Richard Arnesen
Director of Covert Ops
Shrapnel Games
http://www.shrapnelgames.com