The team had a 3 hour meeting the other day, and we came to the conclusion that due to copyright issues we can not make a game in the Naruto universe itself. Instead, we will be creating a game which is "inspired" by Naruto. Think of it as an alternate universe fanfiction.
This will give us more freedom as well as creative control of the world itself. Your clan and jutsu suggestions will become a major part in the game world; as we can no longer put clans such as the Uchiha in-game. This does not mean that the concepts will not exist, but the actual clan will not exist. Things such as taijutsu, ninjutsu, etc, are not owned by the Naruto universe and are a part of Japan's lore, which means they are free to use.