I spent a long time thinking that piloting a cruiser/cap ship is boring and a waste of my time/skills. In fact, that's still true, but now I enjoy it.
See, I originally played this game using Medussa/ Hyperion / wolf fleets. Nothing but those ships and maybe a tempest. It's a lot of fun, and very challenging against the larger fleets. But it's eventually boring. So I upgraded to a Cruiser, and I shortly decided the speed loss wasn't worth the firepower increase. So I went to a cap ship. (the high tech arrow shaped one, aurora?) I put a couple tach lances on it, and I have a grand old time destroying fighter wings and frigates.
Now I'm using the TTmod/Gun Runners/ Starwars / Junk Pirates (all at the same time, it's a busy system). I find the SW cap ships to be a dream come true. Slowish, heavy, with massive flux capacity and fairly slow venting. Even with the shields down you can take a very serious pounding and still be in the fight. It is, in short, what I think cap ships should be aiming for in StarFarer.
I really like the dynamic the stock game has going, what with cap ships being bad mofo's and strike craft being their obvious counterpoint. I just would like to see cap ships be a little more... capital. They require very serious resources to build/outfit/fly... they should require very serious firepower to be threatened.
In the stock game, 5 wings of bombers (daggers) can take on any single capital ship in the game, and have a good chance of winning. Those are the cheapest bombers, and they generally won't all come home. But any chump can field 5 wings against a paragon and win. That seems a little off if you ask me. Now obviously this is speculation in vacuum, literally. I say that because if the paragon has proper escorts (as they often do not), it'll eat your bombers for lunch and then come after you. Also, a ballistic cruiser with flaks is pretty much 100% strike craft proof. There is no energy weapon equivalent.