So, a few ideas:

1. Since this focuses on nanites, maybe (very few) nanite worlds scattered in the galaxy?
   
2. A habbitat that is there if you have Planetary Diversity: Habbitats, desinged for nanite-world habbitation. Perhaps it requires shield technology, since you are having to hold off swarms of SRN's (Self Replicating Nanobots)
   
3. The colosus weapon should allow that nanite world to be terraformed
   
   • Or, a megastructure that strips the nanites off over the course of, say, 5 years. Producing a whole lot of nanites, and turning it into a terraforming-canidate world?
4. Origins
   1. A machine origin that makes you made out of nanobots. You start on a nanite worlds, have bonuses if you are on a nanite world, everything you make needs nanites, but mining districts on nanite worlds make nanites and minerals.
      
   2. An organic origin similar to the one above, where somehow this species got some of the nanites in them (Like that blight one), but somehow the two of them merged instead of dying. They live on a nanite world, eat both organic material that the swarm let's them keep, and energy. The energy is absorbed the same way the nanites get energy, and they (the nanites) share it with their host, the organic. Everything has nanites in it. Regeneration on ships, albiet much less than the machine one
5. Weapons
   1. a "nanite thrower". It throws blobs of nanites to eat ships. Multiple tiers, large size only
      
   2. Nanite Swarm Shield. It is a point-defense weapon that destroys some projectiles (so long as it's not energy), missiles, and strike-craft. It bypasses most of the shield, and some armor
      
   3. Nanite-Energy beam. It's an energy beam that "carries" nanites. The energy cuts through the armor, and the stpping of the beam on, say, a shield, releases nanites that can go through the shield as the shield focuses on the beam. This allows a very slight (20%? Less?) shield penetration effect.
      
   4. Nanite Artillary: an artillery that is the M.K. 3. It also releases nanites, increasing the damage done to armor. This makes it not just anti-shield! The nanites feed off of energy, so it also does a little more damage to the shields.

If its not too much trouble I'd like to see some story elements for the Great Archailect, as its super cool yet sadly doesn't get much use other than for the research, influence, and empire size reduction. With this new leader system I think there are some great opportunities to expand the personalities of the Archailect and give it purpose beyond the resources it can give, and for gestalts maybe it can be integrated into the hive mind or machine intelligence directly, ascending the collective to incomprehensible heights. If you'd like I can give you ideas, or if you've got stuff of your own no worries. Thanks for making this mod also, its one of my favorites lol

just curious, would it be possible to add a nanite district for the frameworld origin from gigastructural engineering? i mean im able to get a decent supply of nanites without it but it would be cool :)

Make nanite triat upgrades affects EVERY pops in your empire and add new Assimilation species right - nanite upgrading