What is the difference between "flying" and "this creature can only be blocked by creatures with flying"?
I know it's the "simple answer", but I have to add it for completeness' sake!

A creature that "can't be blocked except by creatures with flying" has about half the functionality of a creature with flying.  In terms of its evasive power, it's quite similar to a creature with flying; a little better because it can't be blocked by the likes of Giant Spider, and "super-high-flyers" such as Cloud Elemental.

In terms of its defensive capabilities, however, it's much worse than a flyer, since it can only block ground creatures, never a flyer!  And as David Z rightly points out, it is susceptible to a different class of spells such as Earthquake, while laughing at the likes of Hurricane and Plummet...