To be honest, I like both plots, but LOI didn't have that great a plot, it was pretty bland in generic, until you see the plot twist involving Leon's wife. On the other hand, Rinaldo and Joachim both had great potential (along with Walter with their mutual connection to make the plot much more intresting and flashed out. But They didn't they just hinted of what happened between them, never really giving us a satisfying answer. Then it topped off with Mathias who utterly made the plot completely worhtwhile with his speech condemning God.
LOS is an overall better presentation, and the plot is damn good and enjoyable through out the game. It only fails towards the end... ironic consider this seems to be the reverse of LOI in how they paced it. But it did change up some nice plot elements with death, gods, and angels in a way that struck us with aww, especially with the God Pan who is easily my favorite character in that game.
In the end, the games are a draw to me, but if you were to combine the best aspects of both games plots, you could easily have an award winning plot.