That was the whole point. Each religion is unique (ish) each provide benefits and you should change between them as your needs change. I usually start out with one of the three early religions, move onto Egypt-myth then move on to another later.
The Egypt myth one is overpowered in the sciences, the Viking one in combat. But in actual fact none of them are over powered because they are all about the same.
As to the druid and shaman/animist ones, they were much weaker than any of the others because their missionaries cost as much as a wonder to build and the only way to build any of the buildings was to first build a missionary and then have them build the building. The AI just could not handle it so I changed the buildings and missionaries back to be similar to the other religions in use and construction.
Also I never agreed with the idea of % food bonus was overpowered in other buildings either.
I was toying with the idea that you should only be able to build the cathedral buildings if it was your state religion but could not reconsile that with reality so only did it for druid and shaman religions. I wanted you to be able to build one cathedral building in your nation if you have the religion and more if the religion was a state religion but could not figure a way of doing it.
Anyway if you use AND 1.75 or above kiltech's mod overwrites anything I have in this mod.
I did get half way through making a mod which would make missionaries strategic units by having religions auto spread through out your nation, once they reach it, based on the state religion, size of the city and how many religions were already in the city. That mixed in with my religion decay (original by jekel) would have been interesting.