IRT Choose Religions, I don't think they should all be made equal. In general, all should instead be given more game benefit focus so that none are better or worse than the other but not equal. Yes, they should be a bit more balanced but balanced by preferences rather than some kind of universalism approach such as was utilized in Vanilla or by an assumed tech progression justifying improved religions as time goes on.
With DP considered, every religion should have defined 'flavors' which compares to the leaderheads to determine what religion, after their historical favorite, they attempt to found. I think the trick is to isolate these 'flavors' and determine what each religion should really excel at. I love how different Asatru is from the standard norm, how the early religions do so well with food but not so great at gold, how Voodoo is the strongest for offering production. The original religions suffer a little from being somewhat undifferentiated by default still.
The solution begins with isolating what game benefit feature each religion should bring to the table as their primary 'gift'. Then we adjust the religion's buildings benefits to harmonize with the established intention and make sure that all in all, each is roughly equivalent to the other.