I'd like to see a game that tackles religion the way Brandon Sanderson tackles religion in his Mistborn books.
Give us realistic characters that seriously contemplate the types of questions that real people ask themselves as they go through the human experience. Place those characters in situations that challenge their ideals and provoke thought. Allow the player to experience these ideas in their own way then make real, meaningful choices. Invent new religions, but treat them seriously, exploring the philosophies that are common to most religions without taking sides or trying to direct the audience toward your own biases. This is a difficult path to walk, but I'd love to see a studio pull it off.
IMO the studio that has come the closest to achieving this goal is BioWare. Their talent for placing the player in compelling ethical dilemas is one of the things that keeps me buying their games. I'd love to see a studio with BioWare's talent take on a game that dives deeper into the human religious experience.