1. Nagato - Undoubtedly the most skilled Rinnegan user in the series, solo'd Konoha when using only revived corpses as Pain. The only one to make full use of the Rinnegan's most powerful abilities, and undoubtedly the most powerful Akatsuki.
2. Obito - Skills rival Madara's own, reflecting his past self. His Kamui is extremely useful and powerful, and he has a number of jutsu under his sleeve. I'd put him on equal ranking with Nagato, but I think his misuse of the Rinnegan puts him just a bit below him.
3. Itachi - Obviously very powerful, one of the most skilled ninja to come out of Konoha. Sharingan genjutsu beats most ninja. Susano'o, especially Totsuka, finish the job if that doesn't. However skilled he is, though, he doesn't have the raw power that Obito and Nagato show, so I'm putting him below the two of them.
4. Orochimaru - We didn't see much, if any, of him fighting at full strength, but what we've seen is pretty remarkable, especially since he almost never had all of his jutsu. With the revelation that he can use all five elements, I say he comes off as more powerful and skilled than ever.
5. Sasori - Ostensibly Suna's most powerful ninja, Sasori's assortment of puppets puts him high on the list, especially since just one cut from his blades kills. He's far, far more powerful than people give him credit for, especially since we barely got to see the capabilities of his 100 Puppets Jutsu. His puppet body only adds to that, making him functionally immortal unless killed, and making him immune to pain in general.
6. Deidara - C4 is an absurdly strong jutsu. It takes out... basically anything, and is absurdly tough to get away from. We all know how bullshit his fight with Sasuke was, but that's beside the point. Deidara has an incredible variety in his jutsu, but he himself admitted that Sasori is on another level.
7. Kakuzu - Absurdly strong, absurdly durable, and with enough raw elemental power to level a forest. No denying that Kakuzu is exceptional, but I think the others have the variety card over him.
8. Kisame - Kisame is strong and skilled, with the most powerful Suitons seen in the manga. Samehada only adds more to his power, and his immense levels of chakra make sure he isn't going to tire out. I'd like to put him on equal footing with Kakuzu, but I feel Kakuzu is just a little stronger.
9. Konan - Konan isn't about raw power, she's about how skilled she is with her paper. She's unfortunately low on the list because of that, but I'm not trying to say she isn't formidable-- she just lacks the raw power the rest have, but more than makes up for it in skill.
10. Hidan - Hidan is... a good assassin, but weak comparatively. He doesn't have any of the intense ninjutsu the other have, and instead relies on physical combat and immortality. It's effective, but not as impressive.
11. Zetsu - We haven't seen enough of him to rate him.
