I was reading reviews of the 9.7" review on Ars Technica and apparently the new cover only fits if you use the case. That's so lame as I've used the smart covers for years.
The new Smart Covers are pretty much the same as the old ones, but when you’re just using the cover by itself it hangs over the edge of the tablet just a little when closed in a way that looks and feels a little awkward when you’re handling it. I have dubbed this phenomenon “overflap,” and the overflap seems to be happening because Apple designed this particular Smart Cover to fit better with the Silicone Case rather than the iPad itself. Put on a Silicone Case (which covers the rear of the tablet and joins with the Smart Cover to provide full protection) and the Cover fits perfectly.