Weapon Triangle reworked: Advantage is +100 hit. That's it.
Promotion does not reset level, and the level cap is now 30.
HP can go up to 80 and all other stats can go up to 40 for all characters.
Trading, rescuing, dropping, talking, and support conversations are free actions.
Support Rate increases when two allies are deployed together, once per battle. Supports build faster in later maps.
Support Bonuses are active throughout the entire map, and Affinities give different bonuses (still (unit's affinity bonus + partner's affinity bonus) times support rank, rounded down)
Fire: +0.5 Attack
Ice: +0.5 Defense
Wind: +2.5 Avoid
Thunder: +2.5 Crit
Light: +2.5 Hit
Dark: +2.5 Dodge
Anima: +1 Hit/Avoid/Crit/Dodge
You can steal even if your inventory is full.
EXP gained in battle does not change based on whether a character hits the enemy or not.
All weapons give 1 WEXP, except Training weapons, which give 2.
Multiple S Weapon Ranks can be obtained per character.
S Rank bonuses removed.
Vulneraries fully heal the user.
The Growth Scroll gives +50% to all of a unit's growth rates. It basically just turns a single character of your choice into a monster.
Promotion options changed. See the characters page for details.
Various classes use different weapon types.
Crit bonus upped from 15 to 30. Snipers, Wyvern Knights, and Druids get this bonus.
Desert treasure is guaranteed to be found by all units who are unimpeded by sand, such as mages and fliers. Thieves are unimpeded by sand now, too.
Dancer rings also refresh units.
The Devil Axe's backfire rate is changed to 40 - Luck.
While never explicitly stated in-game, Delilah can use lockpicks and controls the convoy.
Not technically a change, but note that when an item other than a basic weapon type or Vulnerary appears in a shop, it is likely the only place you will get to buy them.