The ability to walk and fly airships in eight directions, as well as through use of the touch screen.
The new summon, Whyt, who replaces Rydia in battle and acts automatically, based on abilities you set it prior to battle. It has infinite MP and will act for approximately 3 turns before dismissing itself.
The Fat Chocobo gives access to five minigames used to increase Whyt's stats, as well as an option to battle your Whyt with a friend's, customize its appearance using the DS touch screen, and change its battle behavior. The Fat Chocobo also lets you listen to the music player, watch previously seen cutscenes and view the bestiary.
The Fat Chocobo no longer holds items, as the inventory space limit has been removed.
Many of the bosses and enemies are much more difficult. In general, enemy HP is increased, new attack patterns are added, enemies do more damage, and they attack in greater numbers. Additionally, many enemies which would not use their more devastating attacks unless they were alone, will now use them at any time, even if other monsters are present. Perhaps to compensate, status spells like Stop and Hold are more effective, and a large majority of enemies and bosses are vulnerable to Slow.
An altered loot system, with items dropped and Stolen from enemies changed.
The player is now incapable of changing the characters' names, as voice acting makes this impossible. Namingway, now unable to change the main cast's names, changes his name throughout the game as you interact with him in various scenes in towns and dungeons. Namingway's misadventures form a game-arcing subquest as the player assists him in finding new meaning to his life and he changes his name to fit his situation.
There is a minimap on the bottom screen, given by Namingway. Exploring 100% of the dungeon floor the map is displaying results in free items. Exploring 100% of all maps in the game rewards the player with a rare augment ability.
The ATB Gauge gains a second red bar indicating the time between selecting an action and the action being performed.
Upon entering the menus in the World Map or in towns, a word bubble appears over the character on screen - whoever is at the "head" of the party, reflecting their thoughts and feelings.
Various abilities have been changed. For example, Yang's Focus no longer attacks for double damage; instead it allows Yang to charge his attack power up to three times, which will increase the damage done by any physical attack he executes. Porom's Cry now lowers enemies' defense stat, and Fusoya's Bless restores MP instead of HP.
Various spell changes. Several spells have altered power or MP costs. Rydia's summons in particular are more powerful than before.
Two optional superbosses, Geryon and Proto-Babil.
A "New Game Plus" feature.