Actually i am just going to Hokkaido for the first time myself, so I have yet to experience either Shikaribetsu or Sounkyo.
I personally thought that Shikaribetsu Kotan is more unique, given that everything is built on ice. I was gonna go in my upcoming trip (which is why I know about how to get there), but I had to can it in the end coz i just couldn't fit it in.
However, the scenary in
Sounkyo is pretty breathtaking I heard.
As for getting to Sounkyo from Shikaribetsu, it depends on where you'll be staying at Sounkyo. If you're staying at Sounkaku Grand Hotel, they have a free shuttle bus ("North Liner Mikumi Bus")between Obihiro and the hotel:
Dep: Obihiro Bus Touch Info Desk(just across from Obihiro Bus Terminal) at 14:30
See here for details (scroll down for Obihiro departure): http://www.sounkaku.co.jp/access_e/bus.html
To get to Obihiro from Shikaribetsu, either take free hotel shuttle bus or Taku Bus (link provided above) to Shintoku JR (then take JR to Obihiro) or to Obihiro JR and walk to bus terminal.
If your hotel does not provide free transport (such info should be available on hotel's official website), then you'll have to take the JR from Shintoku station (closest to Shikaribetsu) to Kamikawa station. From Kamikawa, you'll have to take a bus to the Sounkyo Onsen area and then look for your hotel. I would think most big hotels provide some sort of pick-up or shuttle bus service - check with them.
Hope this helps.