The problem you mention is widely reported. The felt/microsuede side of the SmartCover seems to be responsible (though some people, myself included don't have the problem.) There are many alternatives, but almost all of them incorporate a screen cover with a back protector to which it's permanently attached. Just do a few searches on the Accessories forum and you'll find a number of alternatives. If you want to avoid dust collection, stick with covers that are leather (or some leatherlike) material on the "underneath" side when the cover is in place. Less likely to attract dust and "fluff."
However, if you're looking for a screen cover that has all the features of the SmartCover, (i.e. easily detached, magnetized attachment at the hinger) your choices are very limited. That's because, I'm sure, Apple jealously guards its SmartCover name and design.
The only exception to this general rule I've seen (though there may well be others) is from a "DeFauber Woodshop" on the Etsy website. The cover itself is wood on one side and leather on the other. It's specifically designed to solve the problem you cite. I haven't seen one in person but the maker has several wood choices and the photos are very attractive. As you might expect, it's relatively expensive.
Bubinga iPad 2 Smart Cover by DFauberWoodsmith on Etsy