All depends on who the player is. Myself, I haven't been to Ifrit, Moogle, or been to Darkhold, Cutters Cry and Aurum Vale for any other reason than to get the AF gear on Bard or complete a mission. So currently I tend to stick to my classes when I feel like doing some Leve-questing or such.
However, people also want a progression path through 'end-game' content. What better way than to not undermine those who have managed to get the 'proper' end-game weapons and armour than to have them as seperate progression paths entirely - though of course those lucky enough to be able to do both will probably be better off sticking with Job/Primal weapons in a group situation.
I have a feeling that the Class only gear will have a wider spread of stats, but without any noticeable negative penalties (you wont lose HP to gain Healing Potency or the like, but instead just gain less Potency). Also, this is still a game in redevelopment, there is plenty of time for such systems to make their actual purpose clearer - and unlike the looted gear, you can Materia meld them to customise them to you solo/small group needs.