Geoschmo created a PBW game like this a while back called "The Great Experiment". The story was we were all advanced and warring and an Ancient race came and took all our stuff away and put our stupidest people on colony ships and put us in a new galaxy and told us to behave better.
In practice, we all started in a central system with alot of one-way warp-points leading out. We each had nothing but a colony ship that was built using modified datafiles so it could hold about 200M people and a endless-supply-component. We were then sent on our way. Geo had to manually run the turns until we had all landed because he was using modified files so we did not have to worry about paying maintenance on our colony ship. It made for a fun game as you had to decide where to colonize.
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Originally posted by PDF:
Hmmm, having a col ship at start shouldn't be of much use in standard game IMO but ... if we could have a pair of "super colony ships" in Proportions mod - say things carrying 20 M people and having taken 20 years to build (with a huge hull at awful price) - THIS would be useful 
!
But I suppose having a ship at start can only be made with "scenario", so it could not be widely used, too bad ... 