Amegakure, Otogakure, and the Akatsuki vs The Five Great Nations?
Depends on the field of play. If it's a lightning strike and they just blitz them, I'd say a few nations are going to be wiped out.
If they each have prep, Five Great Nations win mid diff. They'd meet on an equal playing field. I.E., no villagers or village to protect. The overwhelming numbers of the Shinobi Alliance would be a key factor. Amegakure would be the first to go, no question.
Iwagakure, Konoha, Suna would gang up on it. Amegakure's shinobi would be cut down fairly easily by the Allied Shinobi, the massive size just makes it hard to get any practical hits in.
Kumokagure can take Otogakure with relative ease, too. Most of them are captured and experimented on freaks of chuunin to Jounin level. Kumokagure has power houses such as Darui, Bee, and A.
The only capable shinobi Otogakure have are Orochimaru, Kabuto, Karin, and Juugo. Suigetsu was held against his will. And not sure if I should include Sasuke in this group.
The Akatsuki is the big threat. If Pein is with Amegakure, then he would probably take out a massive chunk of the combined forces. Amegakure would probably be seiged and blockaded. It would be a waiting game, and Pein and Konan would have to answer and come out.
They would lose. . Sad to say, I love 'em. Kakashi, Gaara, Oonoki, Temari, Kankaro, Gai, Tsunade, Naruto, yamata are all note worthy shinobi that could beat those two mid diff. Yes, Mid Diff.
Kiri would be destroyed, I feel. Akatsuki members: Deidara, Sasori, Kisame, Itachi, could take it.
Kakuzu and Hidan, I'm unsure of where to stack 'em. I feel like they would be stuck with Otogakure as to help them and make their allies survive.
Once Amegakure falls, the shinobi would then begin to work their way to Otogakure.
The remaining Akatsuki would fall back and hope to defend their ally, Obito. . I forgot about but I'll stick him here too.
I see this being a very long, deadly battle in the Land Of Rice. Each Akatsuki member being taken out one by one, with extreme difficulty. Deidara himself would take out an entire regiment with his final blow.
Chiyo, kakashi, Sakura, and Kankaro can take Sasori down, the next biggest threat in a war.
Kisame is countered by Gai or a Bee.
Itachi will be overwhelmed the minute he steps foot on the battle field. By the time he uses Amaterasu and devistated the allied forces, he will be low on Chakra and I'm certain not every shinobi will be hit.
Hidan. . .Is an ace in this war, but would probably be kidnapped for intel after he is defeated by a group of ninja.
Kakuzu would be defeated by A, most likely.
Obito, Orochimaru, and a select few Otogakure uppers would be the last line and obviously... Lose.