I was playing another game recently (name withheld due to forum rules) and learned of this mastery system. Each class in the game gets their own masteries and they are used in various ways. Here's a picture for a general idea:

In the above image you see various skills and specs for the Gunslinger class. For each section you can only set one modification. You can change them/equip different modifications at will outside of battle.
I'll explain each part and give examples of their effects in this spoiler:
General Skills: Modifies your primary skills. Examples: Primary attack has +15% damage, primary attack has +25% accuracy, secondary attack reduces monsters defense by 5%, etc.
Attack Spec: Modifies your offenses. Examples: damage+5%, auto-attack/GCD speed+5%, crit rate+5%, etc.
Advanced Skills: Modifies special skills. Examples: Trap is 5 levels higher than you, Trap increases your movement speed, charm lasts longer, etc.
Defense Spec: Modifies your defenses. Examples: HP+5%, Defense+5%, Recover 1% HP each time you're hit, etc.
Tactical Spec: Modifies your support. Examples: Each hit has a 25% chance to lower targets defense/move speed/healing recieved/etc.
Special Skills: Modifies you uniquely. Examples: Adds 1% of your attack to your defense (Gunslinger also can learn a trait that adds 7% of your defense to your critical hit rate), flat increase to attack and enmity reduction, etc.
Now the game I'm referencing is a game that focuses on using various stat builds so the above would obviously work differently in FFXIV. In FFXIV everyone has the same skills and there are no skill trees (which is a good thing) but I think using this method would be a way to bring in a bit of uniqueness to our characters.
An example of how I could see this being used for Archer/BRD in the following spoiler:
General Skills: Heavy Shot potency +X, Heavy Shot accuracy+X, Misery's End lowers X stat of target, etc.
Attack Spec: Skill speed+X, Accuracy+X, Crit damage+X, etc.
Advanced Skills: Repelling Shot Distance +X yalms, Quick Knock radius +X yalms, etc.
Defense Spec: VIT+X, Recover X HP each time you're hit, X% chance to increase movement speed by +X when hit with an attack etc.
Tactical Spec: Each hit has X% chance to lower target's accuracy by X, each hit """""" critical hit rate by X, each hit """""" skill/spell speed by X, etc.
Special Skills: Requiem range +X yalms, Ballad range +X yalms, Paeon range +X yalms, all song range +X yalms but lower effect and MP drain, all song range -X yalms but stronger effect and MP drain etc.
Some areas (like the Tactical Spec examples) would obviously need to be limited to 1 activation every minute or so. I think this would allow for a bit of optimization in whatever gearset you happen to get lucky with in drops or melds as well. If your current set is heavy on accuracy you could set your Attack Spec to crit rate; if your current set is heavy on crit rate you could set crit damage; if your set doesn't give you enough accuracy for the current boss you could set accuracy. With the way this game is played it might need to see further restrictions as well such as being locked into your current choices for a certain period of time or maybe using a similar reset option that we have for our stats.
This system could also be used on a cosmetic level (either in lieu of or in addition to the above). By doing various class/job quests (or maybe even as subscription bonuses like they did with minions) you could unlock new appearances for your skills. Sick of Ruin's color scheme? Perhaps a "Glamour Spec" option could be added to change the color of it. Hate the SMN egi appearance? Perhaps you could instead equip a new skin for them.