In SO3, they don't gradually, or slowly learn they're actually in a game. It happens very suddenly.
See, I might almost envision it as paralleled through our own experiences as humans.
Perhaps a trilogy. The first would be largely dominated by religion and exist in a very traditional RPG world. Your character perhaps acts to fight the church and it's suppression of science. Insert "magical" element for sake of separation from our own reality and to establish an actual sense of godliness within the game.
Then the second game details the world's tumultuous evolution into a more scientific world. Perhaps there's a hyper progression of scientific achievement through preparation for an unavoidable catastrophe. Maybe your character works to unify the world by mid game. Get crazy with the end boss being symbolic of religious ideologies and you can only defeat them with physical attacks. Game ends with the founding of the first space colonies.
Final game is entirely sci-fi with absolutely no "magical" element, no trace of god. Until the very end when the presence of a god being is almost too certain. Only for that god being to end up being us.
Actually, you have just vaguely described the star ocean series without meaning too. :u The first one is a very traditional RPG with sci-fi elements popping up throughout. The second expands on it and delves more into the sci-fi concepts and ends with a bunch of religious symbolism. The third one is basically as you described as well (eerily so) but there are still magical elements in the underdeveloped planets. ---