I personally feel as though there will be a new villain, although I do hope they'll try to branch out a little more with their villain types. I love Ghirahim, Chancellor Cole, and Yuga, but they all are similar in my eyes in their execution. Ganondorf could be involved, but I'm not honestly too sure, I hope he has an interesting plotline, unlike his last appearance (not counting ALBW) in TP. I guess what I'm trying to say here is that it'll probably be someone new.
I personally hope that it's something they haven't done before.