Well i actually think, that the previous Wing Commanders all have a better capship system than Prophecy, yes.
Or to better say, the Prophecy system was a good idea, that went bad. Actually i never know, why an engine should be a critical subsystem you have to destroy to kill a capship. But the main problem in this was the fact, that you were not able to destroy these systems with prolonged fire of your primaries... it had to be a weapon with the "bomb" flag.. to speak it in freespace terms. Actually that you are not able to kill Capships in Freespace 2 with your primaries was also a bad idea IMO... it should be possible, but should only take longer.
Maybe not worth the effort in time, but at least in Silent Hunter 3 i was out of Torpedos and was still able to complete my mission after i sunk that god damn carrier with my on board cannon.
But i have to say, that i think that the general hull system of Freespace is not much better.. it does not matter where the last shot is placed.. the ship explodes, even you hit a region of the hull that was not punched before.
I think the System with the 4 segments in WC1-4 was much better... you were only able to kill a capship if you have caused enough damage in that specific segment.
I think the only game that made this one better than all other games was Klingon Academy IIRC. Actually its damage system is still the best in this genre.