You can't even compare the Sidewinder Freestlye to the Wii. Firstly, it's a tilt sensitive controller like the PS3s. That's different from physical movement in 3d space; the difference between tilting your hand and pointing, I'd say.
More importantly, there's one key difference, and one that will come into play with Red Steel, MP, etc (let's also not ignore that a) these games are in development and b) people also need to get used to it), is that the Wii controller is a guarenteed peripheral. Developers know it's there, and thus exactly what they can do with it.
As an aside, I have read the mixed reports; one that aiming (but not using the melee combat, which was apparently very intuitive) in Red Steel was iffy, another that Zelda was uncomfortable, and another that said Metroid Prime was the Dogs Nadgers.
Primarily, though, it's daft to suggest the input method 'doesn't matter'. Of course it matters. If it didn't matter, we'd all be using single-button joysticks or keyboards sans mice. Hell, just look at the DS touchscreen as an example of different input methods mattering. Look at the endgame; get it right, and instead of tapping B in Zelda, you're swinging a sword. Or rather than holding L or whatever to aim and tighten your bowstring, you pull pack, wait for the controller speaker to 'snap', then let go. Now, it's not easy, but if you do it makes gaming ten times more immersive and hence fun. Thats why it matters, and that's why it's a threat (well, aside from the prospect of simply bypassing them and opening a massive new market, as kara mentioned was key to the PS1 and 2) to MS and Sony, even if they won't admit it - because if you make it physically immersive, then the graphical difference begins to vanish and even be overridden, and the advantage of the 'HD' systems in the main markets can be eroded.
Gameplay. With any luck, Nintendo will get it right, and it'll be the wave of the future. Or I guess we can play 20 carbon-copy shooters with oversized crotchplates and high-res textures, because it doesn't look like anyone else is trying to innovate the way we play games.