You nailed it. Right after Pain died, the story made a dramatic and terrible shift. The whole kage summit was slow, then it just became so disjointed and really hard to believe in the conflict between Naruto and Sasuke. Part of me feels like Pain was supposed to be the real last villain. This who Tobi and Madara business seems painfully tacked on. If you read the manga, then you know how much they are undoing in the basic story just to keep this crummy arc afloat.