I beat Skyward Sword sitting on my couch the whole time. Are you using an actual Wiimote plus, or an offbrand like the Nyko Wand +? Cuz those offbrand controllers suck, especially the ones with the motion plus built in. Nintendo's official controllers with motion plus built in get that shit done right though.
However, did you try looking for a cheat file with Accio Hacks (or the cheat downloader in cfg usb loader)? Some games have cheats that reconfigure waggle to buttons on a classic controller (pro) such as Donkey Kong Country Returns. I'm not sure if anyone ever did so for Skyward Sword (as personally I found those controls quite innovative and intuitive), but its worth checking out if you really are struggling to play the game.