Yes, yes, yes. The syncreticism tenets should do more for their opportunity cost of picking it over other tenets. They should ALSO count-as requirements for some achievements and decisions. If I'm wasting a slot to roleplay my realm intermingling with another religion, they should at least do something more useful than a mere opinion bonus and the ability to use their trinkets. IIRC using artifacts of the religion you're syncretic with wasn't even a thing before a recent patch, and I think it's a step to the right direction.
It doesn't even protect you from Holy Wars so what gives?
As for shared holy sites from Syncreticism, I would LOVE it but I'm not sure if it would be easy to implement. Would be nice to have usuable pagan holy sites in the middle of no where as a christian or muslim. Because as of now Holy Sites are just too static and creating custom faiths of in an area remote to your religion means you won't even be able to have head of faiths of your own.