The Zodiac Job System - There are now twelve License Boards, each one representing a job. Once a character chooses a job it cannot be changed. Isolated licenses can be accessed by unlocking Espers and Quickenings.
Trial Mode - The party must fight through 100 stages, each one containing stronger monsters. Completing this mode unlocks New Game+: Weak Mode.
Controllable Guests - Guest characters now be controlled, and their gambits can be edited. Their equipment cannot be removed.
Controllable Espers - Espers can be controlled once summoned, and their gambits can be edited. The player can use their ultimate attack at will.
Speed Boost - Pressing the Playstation-Button-L1 speeds up the game, making getting around easier. The music and cutscenes still play at normal speed.
Gambit Changes - There are 16 new gambits. All the gambits can be bought upon leaving Barheim Passage.
Item Changes - New items have been added, and some of their effects have been slightly changed.
Enemy Changes - Enemies have been changed slightly, plus new enemies have been added. A battle against all five Judge Magisters is also included.
Magick Changes - Water and Watera are renamed to Aqua and Aquara. Many spells have been re-categorized; Bravery and Faith are now White Magick for example. Cure and all tier 1 Black Magick elemental spells have an area of effect (same as their higher tier counterpart) instead of targeting only a single unit. Not all magick can be bought, and some must be found in treasure chests.
Equipment Changes - New weapons have been added, like the Excalipoor, while others have been slightly changed. Armor and accessories have also been slightly changed. Some weapons have different elemental alignments.
Shop Listings - Some shops have had their inventory changed.
Hunt Reward Changes - Rewards for defeating Marks have slightly changed.
Mist Knack (Quickening) Changes - Mist knacks no longer take up MP. Instead, they have their own Mist gauge.
MP Changes - Since Mist Knacks do not use MP now, obtaining Mist Knacks does not increase MP. Instead, characters simply get more MP as they level up. Max MP is determined by the character's job.
New Game+ - Two New Game+ modes are available. Strong Mode, where all characters begin at level 90, and Weak Mode, where all characters begin at level 1 and never level up. Nothing carries over into these new save files.
Treasure Respawns - Treasures pots now respawn by just moving one screen away.
Treasure Item Changes - Some items inside coffers have been switched around, added, or removed.
Break Damage Limit - There is no damage limit anymore. If a character does more than 9,999 damage, the game will show it. Against weak enemies, it is possible to achieve over 100,000 HP of damage with a single attack. This gives the strongest magick spells greater potency to rival melee attack with high hit combo.