I just spent a few days playing this wonderful game again and wanted to give my few cents about the latest changes.
As a long time player since 2014, the way this game progresses feels fantastic. Most of the changes are very welcome and it approaches a finished flair.
While few years back i felt it was necessary to play with mods, because a lot of core features were still under development, i usually find myself just playing the base game nowadays, because it is fun on its own.
Things i have issues with are few, but one example though is the fleet headquarters taking up an industry slot. I feel like this unnecessarily takes from the fun factor of the late game, one of wich was seeing your own empires fleets all over the place. I understand you did this to kind of limit the late game impact of colonies, but i don't think most of the time the fleet headquarters benefits warrant the use of an industry slot, so the change just keeps the players from having these fine large faction fleets flying around.
So my suggestion at this point is to either remove the need for an industry slot (maybe offset by higher sustained cost), or making the headquarter more beneficial by allowing it to spawn expeditions. Maybe having the option to plan and spawn your own Faction-style expeditionary fleets, to attack known pirate/pather bases, or to impair another factions market share of some goods could be a fun addition. That also coincides with the headquarters description of projecting power throughout the sector.