Ok: on the Pirate colony issue:
1) Pirates should be able to build their own colony ships only.
2) Pirates Should be able to use captured enemy colony ships only.
3) BOTH!
4) NEITHER!
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#4 is clearly not a viable option
#3 is built in to SE
#2 is my opinion
#1 is going to be very hard to mod. (ie. impossible)
My view: Think of pirates on earth. A colony in the new world is wanted.
Pirates aren't going to be setting up colonies in the new world, since they just can't organize anything major like that, and provide supplies & money.
But if they happened to come upon one of England's colonization fleets, and captured them, the pirates would have everything they needed.
Of course, the colony they created would tend to be an easy target (no large country backing them up) and they'd be nuked to glass after a few turns.
Sorry for mixing Modern & historical like that wooden fort/city getting nuked
