Miyazaki would definitely be my top pick as well.
I feel that Katsura Hashino still flies a bit under the radar although all the games he directed thus far have been really well received (Persona 3, Persona 4 & Catherine). At least I rarely see his name being mentioned.
I also wonder whether Naoki Yoshida (FFXIV) will ever get the chance to direct a FF offline main title in the future. Even though he is currently getting critizised for the current patch cycle you can't deny his accomplishment of reviving a dead MMO. Would be interesting to see his take on an offline FF.