Yeah, that you were able to destruct Capital ships only if you are destroying the Bridge and Engine was a bad idea.
Wing Commander was not very consistent in this one.
In Wing Commander II for example all capital ships were SD Lucifers
You could only damage them with Torpedos at all.
In Wing Commander III you were even able to destroy the Kilrathi Dreadnought with your lasers, even it takes ages, so this was like in the first game. Actually i always liked this principle much more.
In Wing Commander IV however you had something like the capital flag in Freespace 2, which i actually do not like also btw., so that the finishing blow have to be caused by a Torpedo, but you were able to cause 99% hulldamage with your lasers.
And now Prophecy, where you have to destroy specific subsystems to take down a capital ship. And you can damage them only with Torpedos or with the Plasma Gun from the Devastator Bomber, at the end of Prophecy and especially in Secret Ops you were able to kill capital ships without problems with your primaries if you were blessed to get the Devastator... ridiculous because you only need 6 hits to destroy the Nephilim Dreadnought in Secret Ops
That is much quicker than even a whole fleet of GTVA Colossus needs to take down a single Sathanas.