I think the wiimote/nunchuk setup is brilliant. Like others said, it's very comfortable as you can rest your arms apart on your knee or on an arm rest. When I think about it, I'm kind of amazed it wasn't done sooner.

As for fps, I like the pointing or analogue controls. I don't play a lot of fps anyway, so either control method is fine. Although if given the choice, I would go with motion controls.

I really don't think it's as tiring as some make it out to be. Unless you're playing sports. But in that case motion controls are perfect. Although I wouldn't play them for hours. 

I don't really mind motion controls, but I really hate when they are used incorrectly.

For example:

New Super Mario Bros. I really hate the fact you shake the controller to do the spinning jump, and you have to hold 1 while shaking to pick up things.. Sometimes simply by just pressing the buttons you can accidentally spin jump, which leads to a death every now and again..

I do however like the interaction with platforms using motion control. When you tilt the controller it tilts platforms, etc.

Thats a pretty new element to games that make it worth while.

Good example of motion in a hardcore game:
Killzone 2!! The dualshock, despite what people may know, is equipped with accelerometers and a gyro for motion.

The way killzone basically makes you hold the controller still while sniping, or else it causes inaccuracy in the rifle, is a pretty great way to immerse the player in the game. Just like you would in real life, you have to concentrate on the shot and keeping it steady, which is a really good touch on the sniper rifle.

A lot of core games are "hard" or "complicated" because the interaction with the game's interface is difficult. The perfect example of this are the classic Resident Evil games where shooting a zombie was a challenge because you had no way to (really) line up a shot. With a conventional controller you're limited in the level of interactivity you can have in a game by the number of buttons you have, because adding additional functionality beyond that point increases complexity; and eventually the game becomes unaccessable to many people.

Really expressive motion controlls can answer these problems because there is the opportunity to more closely match the interaction with the game's environment than could ever be done using a button; and there is far more functionality that can be added to a game because there are far more potential motions that can be used than there are buttons on a controller.

The challenge (of course) is adding these motion controlls so that they're a meaningful enhancement to the game, and not just adding motion controlls for the sake of adding motion controlls.