For as long as I can remember Command Crusiers have been considered specialty ships.
Specialty ships are made for specific purposes, Command Cruisers are made to command groups of ships. They would be more expensive to build, are built on standard hulls, were fewer in number than their line counterparts due to such expense. They would be worth more if destroyed by an enemy, not just because of their superior construction, but also becuse of the seniority of the officers commanding them who would be regional commanders and damage to an enemies command structure would always carry a higher value. I can't think of this as not being considered a specialty ship by any stretch of the immagination.
As for being categorized, have any commando or scout ships been so categorized before? Does this make them not specialty?
Simply put a Command Cruiser has always been a specialty ship, so if you want to treat them differently than other specialty ships thats fine, but it does not change the fact they they are specialty.
As a side note, if you ever want people to consider flying more line ships far greater distinctions need to be made between the common line ship and the specialty command ship. Not likely to happen over one point difference however even should the command ship be placed with its fellow specialty ships. Line ships would only get wide consideration if they were either free from disengagement penalties, did not count for pvp points, or both.