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I am not sure if there are any indigenous life. However, there are planets that are settled by rival races in the system. Has the game been changed so that if on world in the system is occupied by another faction, I am cannot settle other worlds?
 
I can't seem to choose which planet I want to colonize in a system, the AI just picks one for me. And is there a way to colonize more than one habitable planet in a system?
 
In the lower left corner of the colonize mission screen you "choose" what planet to colonize in a system. This feature has been there from the start... not that confusing to me at least.

Funny when you eventually find this stuff, you wonder how you ever missed it. There is a awful lot of information hidden away on some of those screens, some you right click, others left, some you drag and drop, others you double click. Something like this can take me weeks to get a grip of, but int it good? ;)