Ok, I'm going into a bit more into the backstory behind this game. For everyone curious about how the game will flow, (or just want to know why I'm screwing with the Naruniverse) here's where you want to be.
We chose to make it not follow the plot the the Naruto manga for several reasons. The biggest reason is that it gives us more freedom to work. For example, we can have some mission where Naruto and Gaara's forces are trapped and the two officers must work together to survive despite their differences. The game still works within the same universe (same characters who have the same abilities), but we aren't bound by things like Orochimaru hating Itachi and thus would never work with him, or the timeskip and pre-timeskip characters meeting each other.
Secondly, it balances the game out. The Akatsuki don't really have anything resembling an army in the manga, and would thus be horribly outnumbered if it were just them fighting. Controlling their team would be much harder, and fighting them would be easier. Also, Team's 2 and 3 would have drastically smaller campaigns since the manga's focus is the Leaf Village members.
Finally, it saves us work. We don't have to try and sprite extra members of Akatsuki to balance the teams, nor do we have to recreate the storyline's areas.