The point of having a colony ship may be to avoid confusion among new players. I can see a bunch of new players designing their ships and saying "WTF? Where's the colony ship? How am I supposed to colonize without any colony ships?". That's the only real reason I guess for them existing.
That said, I still use colony ships to colonize

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Courage doesn't always roar. Sometimes courage is that little voice at the end of the day that says "I'll try again tomorrow".
Maturity is knowing you were an idiot in the past. Wisdom is knowing that you'll be an idiot in the future.
Download the
Nosral Confederacy (a shipset based upon the Phong) and the
Tyrellian Imperium, an organic looking shipset I created! (The Nosral are the better of the two [img]/threads/images/Graemlins/Grin.gif[/img] )