Refined my request a bit.
Physical Level - Remove It, Get rid of Point Allotments. Give each skill a Stat and Element it enhances if you have it equipped.
Armoury- Keep It As It Is. Rebalance the skills that are causing problems with people cross classing at high levels.
Job System- Implement it as a bit of a Title System. Each Job Title has 10 Levels. Each Odd Level (1,3,5,7,9) Grants a new Job Specific Skill. Each Even Level (2, 4, 6, 8, 10) Grants a Job Trait. Job Levels are granted by a Point System determined by using your Job in Party Based Events like Behest, Dungeons, Etc. A bit like Faction Points from Leve Quests.
Any Weapon, Any Job A bit like the Subjob system from FFXI, No Weapon Class is restricted from a Job. The Weapon instead alters how the player performs the skills of the Job. the Job Defines the Role, the Weapon Defines how its performed. A Paladin/Gladiator uses a sword and shield to bolster defense. A Paladin/Lancer uses damage dealt to maintain hate. A Paladin/Marauder can maintain the hate of multiple targets all at once. etc. Yes some options will be obviously inferior choices but this should be up to the player to decide not the game. Just like we did in XI with the subjobs.
Bonuses From Stats on Skills based on Jobs- Every Skill is granted a "Familiar" Job. "Cure is Familiar to White Mage, Red Mage, Paladin"'. When you have a skill equipped that is Familiar to your Job, you get double the stats and elemental alignment from the skills you have equipped. Some Skills have a Counter Job. Equipping Skills counter to your current Job remove or lower the stat bonuses from that skill. "Cure is countered by Black Mage, Dark Knight."
Some Jobs are Neutral and do not grant or remove bonuses from skills. "Cure is Neutral to Dragoon, Monk, Thief."
Area of Effect Modifier One of the skills learned by most mage jobs is using a Spell it is Familiar with in a AOE Capacity. Even if your Equipped Class is not a Magic User. "White Mage gets Brilliance. Casts Cure as an AOE from target." "Black Mage Gets Corruption. Casts fire as an AOE from Target."