FS bombers are way more effective than the capital ships they're meant to destroy. Freespace is meant to be enjoyable from a player's point of view as a fighter pilot, as are all space shooters, so capital ships are necessarily nothing more than targets. FS2 ships have impressive flak and beam defense, but what really protects them are the fighters. Try playing Bearbaiting, Slaying Ravanna, or a similar mission without the fighters, and you see how weak the capships really are against proper bombing tactics. I understand the need for large ships for storyline purposes- most players expect a game to have destroyers, cruisers, and even Sath-type ships for the sake of the "oooh, look at that big ship" factor. But ships like the Colossus, although impressive individually, aren't an efficient use of resources. This is because FS2 bombs are rather powerful versus the armor they're meant to destroy. As an example, it takes no more than 20-30 Harbingers to kill a Lucifer (without invincibility, of course). Compare this to the Yamato in 1945, which survived over 100 torpedo and bomb hits.
A light carrier would be ideal, something like a hollowed-out Satis with a fighter bay inside. It could outfight anything fast enough to catch it and outrun anything else.