(Link to possible spoilers for trophy/achievement information)
Based on the list of achievements and trophies for Naruto Ultimate Ninja Storm 3, there seems to be a confirmation of Uchiha Madara. You'll notice that one of the ones listed is titled, "Uchiha Against Five Kage". Those who know the series will recall what part this is referring to. At the very least, it seems as though Madara will make an appearance in the story mode. However it remains to be seen whether or not he will be a playable character.