The Wii's controls are quite interesting. The Pointer feature literally gives developers the chance to completely revolutionize first person and third person targeting, as has been shown in Resident Evil 4 for Wii. And will be shown in Metroid Prime 3: Corruption.
The Wii has also shown how mini-games and simple sports games can become fun games by simple and engaging motion controls.
However, the Wii is limited in the number of buttons available to the gamer, and this either forces developers to map game actions to motions, force button mapping to uncomfortable or difficult to reach buttons, or drop features from the games that would be easy to impliment with traditional games.
Examples of this can be seen in many games, but I would argue non is more noticable than Metroid Prime 3's lack of quick weapon selecting which was a trademark of the series. Sure we won't miss it, but if the game was created for Gamecube it would have probably still been in the series.
Although there are problems with the Wiimote, and that traditional controls are still useful for many game types, including fighting games. The controller is not a fad, but the first generation controller that will led into the future.
The reason being is that it adds a feeling of true interaction with the game that has never before been achieved in a console game...much the same way that the DS adds greater interaction.
In to the future I believe that we will get the next Nintendo system with a greatly refined motion controller with better button placement and the potential to truly become BEST method to play all types of games.