Orochimaru.
Why?
He was the only one who thought killing Nagato was the best thing to do.
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Results:
1. Jiraiya would have returned to the leave with Orochimaru and Tsunade. That could have greatly delayed Oro turning mad. He would have stayed back and worked for the leaf... maybe even be Hokage.
2. Danzo wouldn't have gained such superiority because Oro was aware of his actions and would take him down if he strayed.
3. No Uchiha clan massare. Oro would have just kidnapped Itachi/Sasuke and has his way. Sasuke wouldn't have been an emo. Itachi wouldn't have left.
4. With all that power, he would have legalized forbidden jutsu. Konoha would have become a strong fortress with lethal techs. Oro would have Rinnegan in the end and live a peaceful life as the new SO6P. True peace because everyone is scared of Orochimaru.
5. Oro has no interest in tailed beasts. He would have permanently sealed them in random objects. No Jinchurikis. Kushina does not come to Konoha. Minato never meets her. Naruto is never born.
THE END.
6. No Yahiko+Nagato+Konan, no Akatsuki.
7. Tobi, if not eliminated by happenings of point 1, would not find a readymade group to use and do his dirty-work.
8. Oro was most probably aware of Madara's manipulation of the 4th Mizukage... even better for Konoha... who cares... just get his a good number of sharks for experimentation.
9. No revolution in Amegakure. More war orphans. More experimental subjects. Betterment of Ninjutsu.
10. No Pain to the world. Jiraiya lives... probably even gets married... and maybe has kids... names one of the kids Naruto.

New Story!!!
11. Bijuus not relavant. No world war.
DISCLAIMER: I do not like Orochimaru or his methods. But he is an evil genius not bound by any limitations/emotions/lack of knowledge. Although everyone in the list is awesome in his own right, Orochimaru is a different level in terms of genius.