Do you need live geo-located maps? Google Maps and Here don't offer Japan maps offline caching for legal reasons. You can still download OpenStreetMap data with some offline map apps but you may not have location pins or an easy/quick way to enter the addresses without a Japanese keyboard installed.
A mobile data connection might come in useful for Kyoto and country areas. You can usually use the wifi at a combini through boingo which I think uses wi2/docomo or by registering an account ahead of time for free. It can feel like a combini is on every corner in Japan, which can be true in certain areas, but more remote areas may not have any or just a few.
If you just want to make VOIP phone calls to outside the country, wifi should be fine. Many newer business hotels have wifi but a small inexpensive travel router occasionally comes in handy.
B-Mobile 14 day prepaid sim does not support VOIP.
http://www.bmobile.ne.jp/english/faq.html
IIJMio visitor sim doesn't expressly prohibit VOIP
https://t.iijmio.jp/en/qa/index.html
So-net visitor sim doesn't expressly prohibit VOIP
http://www.so-net.ne.jp/prepaid/en/index.html#faq