There are several new customizations in Sins2:
1. Primary Color
2. Secondary Color
3. Player Logos on the ship (coming soon)
4. Minimal Color options (ala Sins1)
5. Ships Components (these are items you can buy to tweak your ship stats and abilities).
We felt anything more sophisticated would be too complicated give the real-time size and scope of the game
Anything regarding flagships yet? A couple months back I asked and it was still under consideration (like other victory types).
It would be an amazing free feature, DLC or mod to be able to heavily be able to customize a flagship (or other 'unique' ship). I think that for now this could best be done by mutually exclusive technologies (brand new tree), working on unlocking unique components, abilities (not sure whether that's possible, I haven't looked into anything yet but I assume the hardcap of 4 abilities from 1 is not present anymore?), stat buffs and the addition of weapons on the ship.