The default hulls generally do not have the best weapons, engines, armor, sensors, life support etc that your empire has. If you use the default ships, therefore, then you will miss out on the fruits of your hard-won technology.

Also, the default ships are not optimized for what you need to do. For instance, do you REALLY need to get colony ships out and have them go as fast as possible? Then you need the best engines you have. Do you absolutely have to have the best fighter to fight the evil (fill in the blank)? Then you need to select one of the hulls and load it up with the best weapons and armor you can.

Moreover, you can customize your ships to particular opponents. For instance, if your enemy the Altarians has beams and armor then you want to have shields (to deflect some of their beam damage) and missiles or beams (which will cut through his armor, which is fully effective against mass drivers but not beams or missiles).

Plus, fiddling with ships, components etc is truly one of the wondrous features of GalCiv2. Some folks are true artists – visit the Ship Design thread to see for yourself. I am amazed and humbled at what people can do. Even if you don’t end up being a ship artist, tt is fun to try to optimize components, cost, and mission of each ship – a learning experience, to be sure!

Hydro

you really shouldn't set up each ship as different, but set up a basic class of ship and then build many of them....

You can even use the basic designs of the computer like defenders and just upgrade them, and add your own choice weapons/defenses....

the biggest problem I find with the pre-gen ships is that they fill up the space with alot of stuff you probably don't really want on a warship. Range/life support, etc.

you can use small and tiny ships and throw on some colony modules, and it will cost significantly less than what they want to charge you for a colony ship...