People will hate me for this, but I like the Madara/Obito arc better than the Pain arc. To me, the Pain arc was way too slow, and the art was more subdued. Madara is a very entertaining villain (attitude + one-liners), and Obito is basically a better-written version of Nagato. Say what you will about the annoying inconsistencies in Obito's character, he still has a way more developed backstory, a better explanation for his motives, and had a more believeable redemption. Obito also has better ties as an antithesis to the main characters.
The problem was that the War Arc prior to Madara joining was mostly crap, with half-assed, non-threatening filler battles with no tension. Plus the Kaguya fight was badly-executed, and likewise felt too "easy." Finally, Madara actually became less threatening as a Juubi Jin; he never really fought seriously. Obito was a far more threatening JJ. I guess Kishi was always building up to his Kaguya fight, and never intended to give Madara an all-out battle, but it's a shame.