Although not properly on the topic of number of books available (for which I ascribe to the "who cares what's on Sony store, I've never bought a single book *there*), my thoughts on the two are simpler.
I must admit like the fact that the Sony is thinner, and is almost entirely reading surface, with no keyboard, etc. I use it to read books. Period. I don't need a dictionary, a thesaurus, or anything else. I don't honestly need to e-slurp books off the store directly; I can do the extra steps once a month to get another couple dozen books!
Not that those are bad features, their really quite cool, but it eats into my reading surface, which I find hard to forgive.
For me, the ideal reader would be close to 100% reading surface (controls on edges), with faster e-paper, with better variety of format support without pre-conversion.
With that, the Sony is a bit closer to what I want. Unfortunately, by comparison, Sony couldn't market their way out of a wet paper bag.