I was under the impression the Higaarans rebuilt the mothership simply because it was a known working hyperspace design. Given the state of things in the beginning of the game, they probably didn't have time to design a new hyperspace capable warship, let alone test the design. Given the consequences of failure, a known working, if suboptimal mothership which is capable of creating ships to do it's fighting for it certainly beats out a completely untested warship.
IIRC, homeworld 2 based it's difficulty on the total value of your fleet in RU.
And there's a fan patch out for HW1, that does nothing but change the layout of the parade formation, simply because people captured so many ships that the formation was putting ships completely off the map and crashing the game.
So much you could do in HW1. Besides the grand theft auto, you could get those beautiful missile vettes, and then there was the trick on Sea of Lost Souls that let you get around the fleet build limit.