A lot of time when you add religion to a game it can make a lot of people apprehensive to it. You have people who are very religious in their life and they find the role of playing someone who worships another deity it can make them uncomfortable or make them shun the game entirely. You also have the anti-theist type people who despise religion and wont play it due to those facts. You also have to understand that designing games is a business, we aren't going to make changes that are going to alienate a huge chunk of players because that's a lot of money out of ours and the publisher's pocket. So you have to think of ways to add in a new experience without alienating groups of people. What you do instead of having a very in-depth religious system is you remove the Gods from the actual story and game play and just explain them with your character history and allow that to let you include the really cool classes religion provides.
Plus the apatheists among us will forget about the whole religion/magic system, and thus be at a disadvantage