The USB thing was always just a prototype. Even before they got the alpha boards it was broadly advertised that the footprint goal of the final product would be credit card sized. I'm not really sure how that one took you by surprise
Regardless, to answer your question, there are several key differences between the various ultra small form factor PCs and the r-pi. As has been mentioned price is a huge difference, but there's a reason behind the price. R-pi is a non-profit charity. Their whole goal in designing the r-pi has been to get it into the hands of youth not only in their own country, but in developing countries as well. As such they release their product at almost cost, whereas sheevaplug costs 4 times that much just for the basic model (as well it should, they're a for profit business, there's nothing wrong with that).
Additionally, as this page shows there are a ton of i/o differences (the r-pi also comes with a lot of additional internal options beyond just JTAG, such as around 16 GPIO). It also shows that the r-pi is still the smallest form factor when it comes to size verse other options available.
So a quick summary of differences:
Size (R-pi still the smallest)
I/Os (R-pi comes with the most I/O options internally and externally)
Price (R-pi cheaper by a 4 times)
Goal (R-pi is a charity, others are all about that profit margin)