For the skipping planet numbering thing: they get turned into asteroid belts and the numbering doesn't get redone.
1) No
2) Only Precursors, I'll end up turning Invaders on when I am prepared for them (having them before I actually build a ship isn't fun) and Star Swarm have too much possibility for errors and slowing down the game, and they use up my prescious resources.
3) No
4) Generally off, but I build the jumpgates myself.
And another question!
5) Real stars, yes or no. I have them off because I prefer my systems having unique names (Wolf XXX isn't terribly unique), it feels to me like there are more habitable planets and you have a chance of getting a nebula reasonably close (I haven't seen one in a real stars game).
<--- Getting really sick of the looping error messages that prevent you from playing; I get it, the game can't divide by zero, or calculate the travel time for 300 repeat loops of colonist transport, why not just cancel the process and let me continue playing instead of forcing me to log out and back into my computer EVERY DAMN TIME?
Why do you need to do that? Just pressing the button in the error window is enough for me.
Stop posting while I am writing my post damnit!
Real stars still randomly generates the systems, but it chooses the star from a list of real ones.