Exactly. Just give people freedom. It's not going to end the world.
All the Final Fantasy games reflect in their successors. Doesn't matter if you don't like it. The whole point of the Job System is to reflect that it IS Final Fantasy and pull favorite parts from past FF games that people enjoy. Same reason they are bringing materia to XIV. This isn't VII right?
Classes are already unique. The Job System isn't being implemented to fix Classes. Its being implemented to increase player Nostalgia and to set defined Roles for players to follow should they chose. Roles don't define the weapon you use, just the tasks you perform in combat. Your a white mage, so you heal, Doesn't matter what weapon you equip your going to heal.
The Materia system is simply a "crafting" system that lets you modify a weapon with stones to give you benefits. In FFVII it gave you skills, traits, and stat bonuses. Because skills are already granted by the weapon iteself and in the future jobs. Materia will simply give traits and stat bonuses maybe a few might give skills but that will be rare. Its the same system.