Well let me come with a suggestion then:
How about drop the religions, except for the 'shadow-worshipping' (and rename Religion to shadow). Only the shadow-civs can research the tech, and they will be able to spread it with missionaries.(So you can only get it if you have OB with a Shadow civ or with a civ with 'shadow-worshipping' adopted). Shadow cities will start with the 'religion' when they are build.
If you have 'shadow-worshipping' in your city it will cause unhappiness, but you can purge it with a (expensive?) unit. Having 'shadow-worshipping' in a city also means that the Shadow has city visibility in that city (like in CIV vanilla).
If you have 'shadow-worshipping'in your city and have adopted it, you will receive bonusses, but there should be minusses as well (not sure exactly what this should entail).
Some things to clear stuff up:
- You need to be evil to adopt 'shadow-worshipping'
- You cannot build missionaries untill you have adopted 'shadow-worshipping'
- Only Shadow-civs can research the enabling tech.
- It will spread automatically to new cities from civs who have adopted 'shadow-worshipping', but will have to be spread by missionaries to existing cities and cities of civs who don't have adopted 'shadow-worshipping'.
- It can be purged by a unit which can only be build if you haven't adopted 'shadow-worshipping' and which needs a tech to be build.
- 'shadow-worshipping' in a city without adopting 'shadow-worshipping' as a 'religion' will cause unhappiness, so you can switch out of 'shadow-worshipping', but have to face a lot of unhappiness then.
- 'shadow-worshipping' gives you a big push on the evil slider, redeeming yourself by adopting no-state-religion will put you towards good again, but not as much as you went down upon adopting it in the first place.
- You automatically adopt no-state-religion if you become neutral while you have adopted 'shadow-worshipping'
- There should be civics that are available to anyone not running 'shadow-worshipping', to have some sort of balance mechanism for the benefits 'shadow-worshipping' provides.
- I would probably not have it impact diplo, other then affecting good/evil.
That's all I can think of for now.