Basically the way I envision it is that certain jobs having certain aptitudes towards mastering certain weapons and depending on that aptitude their mastery will vary greatly.
The way I envision it is that certain jobs will have certain talent towards mastering specific weapons, and depending on this talent, their mastery will vary greatly.
This variation would come in the form of hwo your character's stats, such as abilities, critical hit rate, defense, etc, will grow and by how erratic this growth would be. For example, a Red Mage may be able to wield a Great Axe, but because they have no talent woulds that weapon, their skills and abilities will vary greatly. If you play your Red Mage and use a Great Axe as your main weapon, your growth as a character will be very limited, or you'd have no growth at all.
On the other hand, if it was a Warrior using Great Axe then you would, over time, master it. You'd then be able to use specific abilities or attack combo that would not have been possible had you not developed the Great Axe on Warrior.
As for using different weapons, the effect might be in the form of beneifits and drawbacks. Continuing the example of the Great Axe, let's say you were using the Great Axe for a long time. When your character switches to a one handed weapon, you'd gain an increase in sttack speed, since your character has developed their attack speed with Great Axe. Since they've changed to a one handed weapon, the delay would be lower because the weapon is lighter.
However, a drawback might come in the form of the inability to effectively use a shield once you since you are not using one.