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Would be much better if they would just implement a sensible crime and punishment system already.
I will ignore all the talk about griefers and similar topics. I've been thinking about how an alien invasion in ED would/should happen and how the alien NPCs should/would work.
A good crime and punishment system is needed, but an alien invasion would, in my opinion, require a different method to decide what CMDRs get targeted by the alien NPCs.
I'm not sure how it would be the most "realistic". "Realistic" is a bit problematic as this is a game and it's about aliens and those surely should behave in an alien way.
If they (the aliens) start an invasion they aren't that extremely different from us. In that case they would probably target those CMDRs that are the biggest threat first. Since they know nothing about PF ranks they would probably target CMDRs based on the ship the CMDR flies. Corvettes, Anacondas, Cutters, FDL and FAS would probably the prime targets. Those ships would get attacked very often.
The next targets would be big trading ships and only then smaller multipurpose or small combat ships.
If they aim for colonization they would probably try to disrupt the supply routes and destroy all trading ships first and avoid direct confrontations with combat capable ships. Without supplies the combat ships can only be used to protect single systems and get spread out to much. This would make "system hopping" possible for the aliens.
The problem is if the aliens are extremely different from us and have motives that we simply don't understand. In that case everything is possible. They might avoid all human vessels at all cost and only if a CMDR is interfering with whatever the aliens want to achieve that CMDR gets attacked and disabled or destroyed or driven away.
I think FD will go with the first option: Invasion. In that case big combat ships should get constantly attacked by superior alien forces.