I suppose you're talking about OWL. The thing is most programmers look at OWL, see the words class and property and immediately think that it's OOP, that they don't have to look more into it and it has the same problems.
But OWL is not based on OOP, it's based on Description Logic, which is a much more powerful abstraction than OOP and it let's you easily represent things which are very hard with something like Java. OWL includes the concept of complex class, in which you define the logical constraints of the class and then it is inferred automatically by a reasoner. This means that you can build really complex multidimensional hierarchies pretty easily.
For example, you can solve the circle/ellipse this way: the class circle is a complex class which is the intersection of the class ellipse and the class of two dimensional geometric shapes in which both major and minor axis have the same length. Any object that satisfies those constraints is a circle!
About the greek problem: you have to declare that the human class and the complex class which results from the intersection of the class two-legged animal and featherless animal are equivalent. It means that every human is two-legged featherless animal and viceversa.
You can even declare equivalences between ontologies, which lets you build conceptual bridges.
OWL has problems related with the maturity and performance of its implementations, and it remains to be seen if it's possible to treat the web as a gigantic Prolog program, but its conceptual model is powerful and sound.