Madara helped with Obito's downfall, but Obito was the one driving the plot for several hundred chapters. Who was actually the absolute final villain is not crucial to my point; Obito was still very important. Also, apologies about the block text, for some reason the forum isn't letting me create new. @andre:
I don't think his existence as a villain being unlikely is anywhere near a good criticism. It's a bit contrived, but I could see the scenario working in a better work with a little better set up
Actually, there are so many reasons that Obito being a villain makes no sense. Here are just some off the top of my head. 1: Obito just happens to nearly die in an area very conveniently close to Madara. 2: Rin gets killed in an extremely improbable scenario in order to shock Obito as much as possible. 3: Obito, who up to that point had been shown to possess a strong and kind spirit, completely loses his mind and devotes his entire life to the impossible, shot in the dark plan of a man that he hardly knows. Your mileage may vary, but his fall to darkness didn't seem very natural to me. 4: He is able to become incredibly powerful in just a few short years. 5: The Kyubey seems to recognize him when he sees him, for no discernible reason. 6: He acts like a total goofball as Tobi for no discernible reason. 7 His Madara act (that he had little reason to be doing) was so incredibly convincing that he managed to fool everyone, even the Fourth Hokage. His own teacher, one of the people who knew him best in the world. This is made particularly egregious by the fact that Naruto and Sasuke are able to understand each other so well just by trading blows, yet the Fourth Hokage can't even recognize Obito in a similar circumstance. 8: Just in general, Obito is little more than a kid groping around in the dark for a solution, and he manages to turn the entire Ninja World on its head through a mix of unfounded supercompetence and extreme luck. 9: He kept up the Madara act in front of Kabuto, even after Kabuto revealed the coffin that the true Madara was in. Since he's not Madara it's bizarre that he would act like that.