From the same article where Shigeru Miyamoto called Sony's motion-sensing PS3 controller flattering to Nintendo, the legendary game designer criticised both Sony and Microsoft's E3 showing as "the next generation of the same old videogames - it's the same old experiences with new graphics." The quote is, one could guess, a lead-in to lauding Nintendo's new controller: "... and while there are people who enjoy that, we're really talking about the next leap in interactive entertainment, and really bringing interactive entertainment not just to videogame fans but to everyone."
As we have seen with DS games, many hit titles do not use the touch screen, opting instead for a more classic control scheme. Miyamoto's concession ("while there are people who enjoy" last-gen games with next-gen graphical tweaks) might be indicative of many Wii titles not using the system's unique controls to their fullest extent. We laud innovation, but it should be said that forcing developers to add motion-sensing to every title could harm titles that would benefit from more classic controls.
Another point one should make is that all game companies -- Sony, Nintendo, Microsoft, and third-party developers -- have franchises that see very little update with each iteration. Be it Mario Party or Madden, GTA or Quake, some titles see very little change each generation. And all companies are at fault for that.
[update 1: Check out the full interview here -- thanks, that guy!]