Somewhere in this video, maybe halfway through, Sizer (lead developer of FToW) talks about how not only will capships in his mod be very limited (a few per faction, fewer factions, a limited amount for non-affiliated civilians), but even NPC capship spawns will be extremely rare and will only occur when the faction leaders "build" them-- i.e. NPC capship patrols will be under the control of faction leaders.
Near the end of the video when they're at the shipyards, they also talk about capships being constructed by factions at the shipyards and how the partially constructed ship will be visible and vulnerable to attack.
Even these developers (who are soon to release a new mod) predict that Freelancer will be gone in a few years (as a gaming community, replaced by Star Citizen), but they are also showing that an increased amount of realism regarding capships and their use is indeed possible and doesn't break the Freelancer engine.
