With Fire Emblem being any indication (here we go again...), just because waggle and pointing motion is available does not mean it has to be used. For a game like Suikoden, no system really holds an advantage for hosting the game other than marketshare. At most, I could see some Wiimote capabilities for the mini games but nothing beyond that.
Fire Emblem handled it quite nicely though I must admit, giving you the option to use the Wiimote OR a GameCube controller.
That aside, there's still various areas of the game that could be covered. Sindar, Highlands, Harmonia, Nameless Lands to name a few. Viki and Jeanne are still clouded in mystery. It's also possible that previous iterations could be visited in a later time (Grasslands, Dunan, Toran). The possibilities really are endless.