Religious Sects in RPGs
One advantage to your typical RPG religion is there isn't a whole lot of doubt. When you have priests who can heal injuries and turn away vampires, agnosticism and atheism are positions that make absolutely zero sense.
In our own world, despite the claims of various prophets, saints, and the like, we've no conclusive proof of the existence of any supernatural being or beings, much less knowledge of what they might want or expect of lowly mortals. Moreover, even within a given religion, there is a lot of disagreement. You can find the greatest disagreement among people who are essentially in agreement - consider the great controversy in the news as I write this with the Anglican leadership censuring the Episcopal church for its permitting same-sex marriages. Watch the debates between liberal and conservative Catholics on matters like economic policy, immigration, birth control, etc. The Thirty Years War devastated Europe, a war with religious differences between Catholics and Protestants at its very center.
This is something that is rarely explored outside of historical RPGs (for example, Clockwork and Chivalry puts the religious differences between Catholics and Protestants as a major component). You don't, for example, see great disagreement among priests of St. Cuthbert or Mystra. In the established D&D settings I'd suggest that Eberron offers the greatest possibility for this sort of conflict - while clerics get spells, no one quite knows how they do nor does anyone really know if the deities actually exist. Such ambiguity opens all sorts of possibilities, possibilities where your greatest foe worships the same deity.