I can understand both sentiment. I feel the effort spent in FS2 to make them feel like something more than a big target to destroy or defend was well spent - I could spend the day listing all the positives that came with it, but it did cut into the amount of time spent on pure old-school dogfighting. Personally, I tend to lean more in favor of using capships. Outside their awesome factor, I feel that they are easier to build around than most other potential Targets of Interest - non-combattants are usually fragile, big space stations or disabled warships should probably be comparatively rare.
In the end though, capships are only one tool in the mission designer's toolbox, and FS2 itself tread rather carefully around them, and didn't hesitate to tweak them as the mission required. The Aeolus famously never makes an appearance at full power; there's quite a few TerSlash that get replaced by the weaker GreenBeam; the Rakshasa rarely appears with all three SReds; the Lilith only appears once; the Ravana, Sathanas and Hatshepsut are so powerful that most of their fights are thoroughly scripted to either wipe out their target instantly or to make sure that they don't.
You generally do not want to let warships do anything under their own control except for fire anti-fighter weapons. Everything else should be scripted.
I'm
usually fine with them firing their big guns at will, but I certainly would recommend mission designers to not hesitate to beam/turret-lock them and go manual at dramatic moment, eg. simulate lucky shots/critical hits, decreasing performance as damage piles up, perform alpha strikes, or even script every shot in a given battle if necessary.
One of my dream goals for BP2 Act 4 is to have a fully consistent set of 'advanced' warship behaviors, unifying their jump charge, turret ROF, armor class, ECM state, and damage control into one coherent model that players can interact with and learn, rather than doing it on an ad-hoc basis per mission.
I think quite a few of us have had that dream

It was one of my underlying goals back when I started working on an ability manager many years ago, I wanted to be able to have all ships of certain types/variants be able to use BP-style abilities in any given mission if I wanted to, so that all that stuff would be somewhat consistent from mission to mission.