You may also look at the overall model (flat structure or hierarchical structure), the object properties and the datatype properties (how are they used, if the same concept is modelled in different ways), at business rules, if available, and at the DL expressivity.
In which language are the ontologies that you're comparing?
I would say that the answer heavily depends on the purpose of the comparison. i.e. are you looking for a similarity measure? Are you trying to find out which one better suits your needs?
Once you define why you are comparing them, extracting the right criteria becomes more intuitive.