I think the fundamental reason is historic. The airway structure in the days of turbo-charged pistons and the like had a practical upper limit of about 25000 ft. When jets were introduced they could go faster and higher and upper routes were introduced to cater for their operations. And the distinction remains to this day.
Today the performance of propeller-driven aircraft is similar to some lower performance jet aircraft and the need for different route structures doesn't really exist in many areas. This is evident because upper and lower routes are coincident in many cases.
More recent innovations such as RNAV have probably been introduced within specific portions of upper or lower airspace as much as a convenience in many cases because there is already a distinction between these blocks of airspace.