Good points. I see that it makes sense now. As for automated defences, they wouldn't be THAT expensive considering how many zillions of dollars one of those fighters or bombers must cost. Think- right now we could probably make those kinds of automated defenses, so they shouldn't cost very much in the future.
And as for the marines vs. engineers thing, in the old sail days ships would carry a large contingent of marines speficically to defeat boarding attempts. Think of how many marines a cruiser must hold. Several hundred? Now how many people can an Elysium hold? Maybe 50 or so?
I noticed that a lot of FS ships, like the escape pods, are designed for personnel transfer but really can't carry many people. In one of the Silent Threat missions where you have to escort your ship's escape pods as the Krios is blown up by the GTI, you're told that "we have 43 people in escape pods" when there are like 10 escape pods out there- each one can fit 4-5 people? So how many people could a little transport hold, vs. how many people are there on a capital ship?
And even if you do capture the thing, like I said before it's probably going to be sabotaged. IMO there has to be some reason that in Freespace nobody ever captures a capital ship for the sake of using it later