Not all agencies count number of dives. NASE counts bottom time - minutes underwater.
It's an interesting distinction. As it was mentioned earlier, in CCR training we're bound to time in water. For instruction, IANTD tells me both the number of dives and the minimum number of minutes that are required (I don't believe this is unique to that agency - correct me if I'm mistaken).
On one hand, bottom time is somewhat uninstructive. The act of simply being at depth and staying there doesn't necessarily practice any specific skill, whereas ascending and descending are arguably the more task loaded portions of the dive. On the other hand, if all you do is up and down then you are depriving yourself the opportunity to experience failures at depth or simply to solve simple problems like navigation.
It seems that having guidance for both rather than either would be better.