First of all,
Thanks for your nice words on Secret-Japan. It is really great to see that the information posted here is useful to people traveling around
Fujiyoshi in Shizuoka-ken is indeed a place I found amazing. At least their onsen, as I did not stay there overnight. I am looking forward to reading your report on this ryokan.
For Mie-ken, I can't be very useful for you. I have been there several times, but never soaked in this prefecture. From what I have heard, Mie-ken is not really the best place for onsen in Japan.
There are two onsen town that I heard of in Mie-ken, and those are Nagashima-onsen (長島温泉) and Yunoyama-onsen (湯のは山温泉). As I said, I have not been there... Hopefully someone else will be more useful!