A big hope for me with ES2 was that the customization options would be revamped. I am not a coder so I am not sure as to the difficulty but I think the following would make custom factions more enjoyable and fix some of the issues with the disconnect (IE, things that don't make sense for your custom faction to have)


Note: These would be individually selectable options when making a custom faction


1)Being able to pick what your faction species looks like, would affect your starting hero, and what they look like in the custom faction screen


2) Being able to pick their ship design separate of this. 

    Bonus for this but not really necessary: Being able to pick each level of ship individually, including picking from minor race/pirate ships


3) Tech tree


4) Music/Theme/Voice


5) Faction Affinity as normal


6) Main quest/storyline


Additional Bonus for the whole idea but really me just being hopeful:


1) Replacing any instance of faction name anywhere including in tech tree/quests with custom faction name.


2)At least one generic main quest that is unspecific as possible, for custom factions, so your immersion isn't broken.