Currently me and about 4-5 other friends of our gaming community have been playing Avorion. We all love the way you are taking the game with the building system.
I had a couple of idea's to help with the feel and complexity of the game.
Give faction's (a.k.a. Fractions for Akagetsu) alliances so attacking a faction could have repercussions.
Allow support from npc alliance members to enter the system based on the amount of attackers (player and player made ships). Since you upset the alliance of the faction already it wouldn't be unexpected.
Navigation Map coloring based on alliance affiliation. (maybe use a pastel color or toggle?) You would still need to fly to a sector to tell who owns it but it would give more life to the Nav Map and you could also introduce other mechanics in the future with intell / missions for this kind of information too.
Icons for the Nav Map to show what is in a sector after exploring. You could just use letters in the beginning. A for asteroid, S for Station(s), etc.
Upgrade points or Research points for guns that are lesser? A way to utilize the old technology in destroying iron guns you have in your inventory since you are using trinium guns as standard now. Allow the points to be used to upgrade the attributes of a wpn?
Random hostile ships (a.k.a Pirates?) I know this is mentioned in your wiki I just didn't know if this is what you thought as well.
I think with the early stage of he game you have done a great job. I have a lot of other ideas but things to implement quicklyish** and objectives down the road are two different breeds. Let me know what you think! Keep up to good work.