If they start from where they left...I think they'll start with Sasuke bringing back Orochimaru, then when they head to Konoha, they'll try to make something to make the war continue from where they left (If they don't actually retcon that ending). Then at some point they'll return to Konoha with Sasuke and the others there, they get the Edo Hokages and maybe they could use Hashirama's story to tack on some normal fights and some boss battle. Then after they go to the battlefield, they return to the war and keep from there until the end (Maybe put on some mob battles with the mini Juubis in between?)
It's likely the very first chapter of the game will consist of a retelling of the fight against Tobi and the Edo Jinchuriki, similar to Storm 3's action-packed prologue. I'd also expect it would be much easier than it was in Storm 3, along with following the canon storyline (Kakashi and Gai appearing, etc).
That would give them a means to disregard the poor ending of Storm 3 and delve straight into the rest of the story. I wouldn't be surprised if they also included another fight with the Gokage against Madara, along with Sasuke's 'fragment' chapter, just for the sake of clarifying what actually happens.