@Minor Annoyance: Civics hasn't been implemented really. Which other MOO2 equivalents did you have in mind?
Feudal/Confederation
Unhappiness without ground troops
2/3 ship cost (1/3 with confederation)
50% research penalty, which would be insane in civ so that could have to be much smaller.
Dictatorship/Imperium
10% bonus to spy defence (20% with Imperium)
Unhappiness without ground troops (Imperium gives a happiness bonus with troops instead)
Imperium gives 50% command points. That just means more free units like the Vassalage civic.
Democracy/Federation
10% spy defence penalty
50% bonus to tax income and research (75% with federation), which would be huge in civ so those numbers would have to change.
Unification/Galactic Unification
15% spying defence bonus
50% food and production bonus (100% with Galactic Unification)
Unification is also supposed to have no unhappiness but that would be too much in civ. So maybe it could just eliminate one kind of unhappiness. Like no unhappiness from buildings, just population. Or none from population, just from building. It's hard to know what's right at this point.
As regards your thoughts on religion/values: just post 'em, I'm curious.
The back story of some of the races gave me an idea for something that could substitute for religion. The Trillarians believe they are descendants of a lost Antarian colony and that's why they are transdimensional. The Alkari's homeworld has artifacts of an Orion colony. In MoO3 the Ithku and I think the Etherians were experiments created by the Antarians and the Humans were said somewhere to believe themselves to be an unaltered species, but have been created by an unknown race as scouts before they attempt to colonize this galaxy, and the fourth humanoid race of MoO3 that was removed was created by another race to destroy the Humans.
So my idea was to have the possible origins of species be religions. The ones I came up with were Antarian descendant, Orion descendant, Antarian creation, Orion creation, Unknown creation, Divine creation and Independent evolution. The problem with that is in civ different religions always dislike each other and want others to convert to their religion, however it might be that a race would want to be the only descendants of the Orions so they should want others to convert away from their religion. Also, would Antarian creations and Antarian descendants really be enemies? So to avoid overhauling the way diplomacy and religion worked, cool though it might be, it would probably have to make the belief apply to the whole galaxy. Meaning if I was an Orion creationist, I believe all races were created by the Orions.
So that's my idea for MoO religions. It would be a neat flavour/backstory thing but I assume it would be a lot of work to replace a system that already works.