You'd have to pair everyone together
Xemnas vs Pein (Superior vs Leader)
Xigbar & Larxene vs Sasori (long range battle & Larxene's fast moments would allow her to get in close whilst helping fend of Sasori's Over Abundance of Puppets attack)
Xaldin vs Konan (Wind vs Paper you be the judge)
Lexeaus & Vexen vs Kisame (Freeze he's main way of attacking and Kisame doesn't stand a chance combine that w/ Lexeaus' strength and it's easily over)
Zexion vs Itachi ( The battle of illusion)
Saix & Axel vs Zetzu (he's a freakin Venus Fly Trap, Fire would help on a grand scale)
Luxord & Demyx vs Kakuzu (Luck & Time limit + 100 clone creation vs mulitple lives)
Marluxia vs Hidan (similar weapons and both deal in the element of Death)
Roxas vs Tobi (The Battle of the new blood )
and it would seem those who have no match up would do best to tag team against an Akatsuki Memeber
The way i see it, Organization XIII would over power the Akatsuki in every way, for the most part anyway xD
*note* I've based this off of what I've seen in Naruto, Naruto Shippuuden, Naruto 2 manga, Kingdom Hearts re:COM & Kingdom Hearts 2 Final Mix