Edit: Added some more notes about deciv's at the very end after >10 hours into a save.
Hopefully it's okay to leave a bit of fan mail here. The last part of my post will be some observations with hotfix 2019-01-09, and some questions about the future of the mod now that we have the 0.9 survey-> colonization game loop.
Here goes: to Histidine, LazyWizard (for LazyLib which Nexerelin depends on), and of course, Zaphide for Exerelin, thank you! I really love this mod. I waited to try 0.9, maybe foolishly, until Nexerelin was released. I'm a big fan of 4X games. And I absolutely adore Mount&Blade because it is the game I dreamed of when I was a child. I view Nexerelin as a way to achieve that fantasy in Starsector and I deeply appreciate your efforts here. I am having a blast building up my fleet, my faction, and competing with the big players in the sector.
Onto some observations: it looks like decivilization may still be a bit of an issue, but it has been lessened to some extent. Currently, in my save, I am more than 4 hours in. All the factions are still around, and only about 5 places have been decivilized. This is an improvement of 8 places deciv'd and 2 factions eliminated that I reported pre-hotfix occurring over a shorter time period.
I am looking forward to seeing the mod evolve the 4X gameplay in 0.9. I looked through the wishlist in the OP. I'm wondering if you have anything to add onto your wishlist now that we have colonization and the surveying system in the game officially (for example, should NPC factions be able to do these two things? Should new factions be able to spawn?). I have looked through the thread about colonization and mostly came across stuff from 2016 or earlier. My apologies if these questions have already been answered.
Edit 2:
NPC colony expeditions appear to be on the Bitbucket Issue Tracker.
Edit:
Played several more hours into my save. Decivs still seem to be a problem, at about 11 now. I guess I'm at >10 hours into this save. Notable decivs include Jangala and Sindria. Ragnar Complex was also deciv'd (is that a standalone station without a planet?). Since it looks like planets can only be deciv'd and not resettled by the AI, decivs will continue to be more problematic over time. I would guess that, given enough time, only a single faction will remain, only holding a handful of worlds, with the rest of the worlds having been deciv'd.
From an NPC faction point of view, the crux is that settlements can only be destroyed, and cannot be resettled. The result of this is that, over time, more and more settlements will be destroyed by decivilization. Even if previously deciv'd worlds could be resettled by AI, I imagine it would be problematic to fine tune the system such that the rate of deciv vs colonization is at least equal. Barring that, I am going to guess most games will go into what is essentially a decivilization spiral. This is what I have been experiencing myself.
If you want to map paint, maybe that's okay, since you can just resettle everything yourself. But I like having multiple factions around so interesting things can happen.