As my contibution to the current RPG carnival, hosted at the dice bag; http://www.thedicebag.com/blog-carnival-round-4-religion/
I want to share a small piece from a game that was close to my heart.
A little background...For almost 6 years, I ran a sci-fantasy d20 game in the Dragonstar universe. It treated religion as a generic thing, with the offical imperial church worshipping the 5 "good" and 5 "evil" facets of the common deities, as a solution to there being 25,000 or so different gods throughtout the empire. These were archetypes of the typical; the father, mother, warrior, judge,merchant - opposed by the reaper, destroyer, trickster, and I cannot immediately recall the rest.
In the games chronology, a new religion had popped up, and it's it was so insidious, the empire had banned it, and actively persecuted it's members. The religion? The Dualist Heresy.
Dualists believed that the 12 facets were simply masks that the creator and the adversary hid behind to further their own unknowable goals. We never had one in the party, but I used several heretic NPC's to keep the storyline rolling along. They often found common cause with the insurrectionists, and terrorism was quite commonplace.
How does this relate to YOU? Well, let's see here. In ANY game one could allow dualist cults to be found. Good or evil people who are simply...different. Mechanically, the only difference (3E) was that you could take ANY domains you wanted that were not in opposition to your alignment, as well as one bonus domain (for a total of 3). While this sounds overpowered, it wasn't in practice, as the persecution and role-playing angles made it a difficult character to play. Add the lack of any "official" church support, and being actively hunted by inquisitors on BOTH sides of the aisle, and things were often...interesting.
I agree there is a bit of a parallel between the heretics and the early days of christianity. Pagan pantheons of nature gods vs. Monotheistic belief - blah, blah, blah. Take it or leave it.
One other little tidbit, Dualists had a feat available (homebrew) of course, that should they survive to see 5th level, allowed them to channel positive OR negative energy...
In exchange for this colossal cosmic power, we have the drawbacks. Must have N as part of your alignment. (small neg.)
Must be recruited, and recruit in turn. (small neg.)
Actively sought out and "re-educated". This was usually a death sentence, as public executions are all the rage during the Red Tyrant's reign. (big neg.)
Fluff heavy, crunch light, what more could anyone want?