Rediscussion of the Civics concept aside, here is what I came up with now initially for no-SR RCs.
The basic concept is to add some effect for cities without the SR, so you only really get those effects when you have no SR. This way nothing needs to be changed in the basic mechanisms. You can have no SR even in the ancient age, it just won't be very beneficial. In the late game it will often be better to have no SR. The AI can understand this.
* effects for SR
- effects for no-SR
+ general effects
Paganism
* can't select this Civic under an SR
- +2
in cities with no religion
- cannot construct any Temple, Monastery, Cathedral, holy city wonder, or any missionaries
Notes: This one is great as long as your cities are irreligious. Afterwards it is a horrible horrible choice.
Organized Religion (Suggested rename: State Doctrine)
* +25% build rate for buildings in cities with SR
* cities with SR can build missionaries without Monasteries
- -10% war unhappiness in cities without SR
- cannot build missionaries or Monasteries in cities without SR
Notes: The only change here to the original effects is you need the SR to build missionaries. This one is a little awkward but with Paganism fixed, we'll probably rarely see an early OR state without the SR in all or most cities. This way the funny effects will only be seen in late-game no-SR states that use this RC to control war unhappiness.
Theocracy (Suggested rename: Forced Compliance)
* +2EXP in cities with SR
+ no non-SR spread
- +3 Stability for each city without the SR
Notes: This one works oddly well. The no non-SR spread turns into no spread of religions at all which makes sense. The added stability means that under an SR the stability you would lose for some cities not following your SR (in a very indirect way) is compensated for, and under no-SR you get a huge boost to stability. That way this RC comes to represent the more aggressive state cults in history, like under Stalin. But it still works the same when you have an SR.
Pacifism (Suggested rename: Gentle Encouragement)
+ higher military maintenance
+ +50%
in all cities
* an additional +50%
in SR cities
- +1
per specialist in non-SR cities
Notes: This will now basically represent governments that are gentle outwards and inwards, encouraging the growth of their people. Cities with and without the SR will thrive in different ways, and having no SR will just mean they all thrive in the same way.
Free Religion (Suggested rename: Pluralism)
+ +1happy per non-State religion in each city
+ 10%
in all cities
Notes: Oddly enough, this one is already designed to work great dualistically. When you still have an SR your cities are slightly less happy (the SR is the only religion that won't give you happiness) but with an SR your rivals may like you more. It's up to you whom to please.
I must say this does not satisfy me entirely, because I think we need to rework the Civics system more thoroughly, especially in the area of RCs. But this would be a nice start.