That is your choice on that. If you want to bring in canon characters, what part of the series would they be from and would people have the choice to play them or would they be NPCs (non-playable characters).
Or would you choose the route that the canon characters are gone (basically like a time after events of the series?) Or something of that sort.
Or... would it be that its like a parallel universe, everything in the naruto universe is the same except the canon characters didn't exist allowing for a unique story with original characters.
Basically its just what you want to do.