I think we are going about this all wrong. We are trying to force the seven current jobs into "classic" FF icons without giving much thought on the actual Armoury System.
I would like to keep the Armoury System as a foundation and then build upon it instead of trying to reinvent it.
1) The need to make Class unique without using what other MMO's have done. Well that's easy. Final Fantasy has a long history of unique character development from Materia to Paradigms. Why should FFXIV be any different? Sadly to do this I think we might have to get rid of Physical Level.
I would say a spider web type grid where you start in the center. Every level you get X amount of points to spend which ever path thru the spider web you choose gaining everything from Stats to abilities and even more hp/mp along the way. This should allow player to develop their own personal class and make them as unique to them.
But we can't forget about the Armoury System though. Once you learn an spells/ability/trait from the Web Grid you'll be able to apply that to any class if it isn't a class specific. Having said that we do need to have the more defining action be class specific as well as Weapon Skills. Otherwise we blur the line of class distinction.
2. Class milestones and how they relate too FF Iconic Jobs. The goal in character develop is terms of FF MMO is become that Iconic Job like Paladin, Black Mage, or Summoner. Well we can do this by focusing on armor instead of talents.
When you hit class milestone level you get rewarded with Iconic Armor that have stats tailored toward that Iconic Class. Let's say you want to make your Conjurer into a Black Mage. Well the Black Mage Armor is going have stat boost that focus on offensive magic rather than defense as well as having abilities that are available only when wearing that armor.
Also let's not forget the Titles that come with it. When you gather all armor piece you unlock the Icon Title you can place over you character telling the world that you are a White Mage.