Now I need to know: How the Akatsuki has splitted? Konan and Nagato probably discovered that "Madara" was actually Obito (a fucking 14 years old child) and, if we use the anime fillers as canon in the AU, was responsable for killing all the original Akatsuki members in the same day that Yahiko died. The Dark Akatsuki is probably now just kidnapping jinchuriki and and keeping them in captivity, since without the Rinnegan they can't extract the Bijuus from inside them using the Gedou Mazou to form the Ten-Tails.
Oh, they haven't exactly split up. Obito/Madara got into the organization and at first Konan and Nagato might even have somewhat agreed with his plans, but after Obito gets the original members killed, they decide this isn't for them.
However they see that this new version of the Akatsuki is a danger, and stay infiltrated, pretending to work with him while planning behind his back. The two get Jiraiya's help along the way and even Itachi joins them (now as a real spy).
In this timeline so far Obito still hasn't captured the other jinchuuriki, Naruto was the first target and (probably thanks to Itachi interfering) they failed to cupture him.