The plot wasn't exactly confusing, just not very good. It seemed like you were just constantly being distracted into doing something else. Really, the main quest was comparable to a string of lengthy side-quests, each getting more and more important until it became apocalyptic.
Also, I have to add something about the feather that I always find annoying; after you get it, it is impossible to remove it from your inventory. It does absolutely nothing besides waste space.