I have thought of Madara as the main villian for quite come time, and the most recent chapters provide some pretty compelling evidence of this.
Madara = Responisble of the deaths of Naruto's parents -> Lead to Naruto being the 9 Tails host and the villiage shunning him
= Involved in Uchiha massacre -> Lead to Sauske's thirst for revenge and falling to the "dark side"
= Leader of Akatsuki -> Lead to capture of Gara, death of Lady Chiyo, death of Asuma, and the death of Jiraiya
Something also occured to me recently (and I'm not sure if there has already been some discussion of this). What became of Hanzo? It was said that Pain defeated him, and yes he did destroy all of Hanzo's forces. I thought that Hanzo had died too until I purchased volume 48 and saw that the final jutsu Hanzo used in his fight with Nagato was some sort of space/time teleportation technique. The only 4 shinobi in the story that have space/time abilities are Madara, the 4th, Kakashi, and Hanzo. Could there be a connection?
I do have one theory.
Hanzo is not Madara... different hair color, eye color, apparent age, etc. However, if Hanzo survived his battle with Nagato, he would have probably started searching for a weapon that would allow him to defeat the Rinnegan. What better than a mostly dead Sharingan user... Obito. Konoha is so protective of it's secrets that this would have been a rare opportunity. Hanzo could have basically rebuilt him to do his bidding, using various jutsu to maintain control. Using the Sharingan, Obito could have copied almost any jutsu, including one that manipulates space and time. That same ability could have then allowed Obito to perfect the jutsu. Hanzo may also have possessed information on the Uchiha clan, possibly passed on to him by Danzo. However, Hanzo may have underestimated the Sharingan's ability to overcome genjutsu, and Obito could have turned on him and destroyed him. Then, instead of destroying Pain as Hanzo had wished, he might have recruited him as the first member of the Akatsuki. With knowledge of the Sage of the 6 Paths, Madara, and a scrambled brain, Obito may have come to want to wipe out Konoha (the villiage that "abandoned" him), the Uchiha (the clan that never embraced him), Rin, (the girl that never loved him) and Minato (the teacher that didn't protect him). He may have left Kakashi alive to suffer the grief of Obito, Minato , and Rin's deaths. One small piece of evidence was Madara referring the 4th as Minato. At the very least, this Madara, is someone that has some intament knowledge of Konoha.
Jiraya fought Hanzo and probably witnessed the space/time ninjutsu. While he was unable to discover how it worked, he may have discussed it with Minato. Minato, being the genius that he was, used the knowledge of seals given to him by Kushina to develop his own space/time ninjutsu. Kakashi witnessed the 4th's jutsu with the Sharingan and was then able to develop his own.
Anyway...........Really tired...yawn........hope this all makes sense.