Inb4 fuck Skyrim.
Personally, I've yet to choose between Skyward Sword and Skyrim, if only because I haven't had time to fully delve into the former - but from what I've played it's superb. The motion controls don't feel forced, the graphics are a nice balance between the 'realistic' (I use the word loosely) Twilight Princess, and the light-hearted whimsicality of Wind Waker. I'm sure that I'll play it, and adore it to shreds when I get round to it, but until then I've played more of Skyrim.
It's a beast of a game as far as I'm concerned, and, having met very few game-breakers (maybe one quest got fucked up?), it's doing admirably at what it set out to do. Leaps ahead of Oblivion, and I'm still having tremendous fun ~80 hours in.
So yeah, I won't decide until I've played more of Skyward Sword, but it's definitely between those two (unless I'm drastically surprised by something in the next 3 weeks).