Can't use ENY as a search criteria, but IIRC, planes that saw heavy usage despite high ENY numbers were adjusted. The most popular planes typically have lower ENY, regardless of some of the past factors in determining a plane's value.
So yeah, basically it's the way it is because HT made it that way. I think initially performance, payload, range, etc were factored in, and that only more recently has use become a primary factor in determining the values.