(EDITED) Animal Summoning I now can bring up to 6 animals instead of 2 or 3 animals in BG1&2EE.
Animal Summoning II now can bring up to 6 animals instead of 1, 2 or 3 animals in BG1&2EE.
Animal Summoning III ow can bring up to 4 animals instead of 2 or 3 animals in BG1&2EE.
Magic Stone deals more damage now: 3d4 points instead of 1d4 points of crushing damage. Also in IWDEE it deals 6d4 points of crushing damage to instead.
(EDITED) Protection from Evil, among other effects, gives immunity to charm-based spells or effects (e.g. Charm Person, Charm Person or Mammal, Domination, and so on) while in BG1&2EE it’s not the case.
The duration of Remove Fear is changed from 1 hour to 1 turn.
The duration of Sanctuary is also changed: instead of 1 turn it lasts only 2 rounds + 1 round/level, i.e. very shortly in the beginning of the game.
Chant in IWDEE, among other effects, reduces damage dice for all effects outside a weapon’s base damage by 1 (so that a 6d6 fireball will do 6d5 damage, and a flaming long sword that deals 1d8+2 slashing plus 1d3 fire damage will deal 1d8+2 slashing plus 1d2 fire damage instead). The priest’s enemies suffer from the opposite effects.
Also, this spell now has a downside: the priest cannot cast any spells for the chant’s duration, and her movement is slowed by half.
Charm Person/Mammal doesn’t have a +3 penalty to a Saving Throw now.
Hold Person now has the duration of 2 rounds/level instead of 1 turn.
Know Alignment (if someone is interested) now is not Instant, it lasts for 1 turn.
Silence in IWDEE is less effective: the spell no longer has a -5 bonus to a Saving Throw.
Slow Poison now not only cures poison but also cures intoxication.
Also, this spell is not available to druids now (but the druids get Poison immunity at the 9th level).
Call Lightning now has the duration of 1 round/level (capped at 11 rounds) instead of 1 turn/level.
Cure Disease now additionally restores 5 HPs.
Dispel Magic now removes magically created items. The description no longer states the spell doesn’t affect spell protections such as Spell Turning and Spell Deflection.
Also, the description no longer states the chance of the dispel succeeding is determined by the level of the caster and the level of the magic being dispelled.
Glyph of Warding in IWDEE is more effective because a successful Saving Throw vs. Spell doesn’t let to escape the effects of the glyph – instead, it halves the damage.
Holy Smite and Unholy Blight, instead, are less effective: now they give 1d6 magic damage for every 2 levels of the caster, and not for every level, also they’re capped at a maximum of 5d6 at level 10.
Protection from Fire now lasts 1 turn/level instead of 3 rounds + 1 round/level.
Animate Dead now summons not one skeleton that improves with levels, but 1d6 skeletons or zombie.
Also, I would like to mention that the overall summoning limit in IWDEE is 6, not 5, creatures simultaneously.
Rigid Thinking now has the duration of 1 round/level instead of 1 turn.
Strength of One now lasts 7 rounds instead of 1 turn.
Mass Cure is now called “Mass Cure Light Wounds”.
Entangle has no longer +3 to save penalty.
Sunray works differently: it lasts for 4 rounds, it is only usable by druids, and it doesn't have a chance of outright destroying undead
Goodberry heals 5 health/use but you only get 1 item when it is cast.
There're now spells that can be cast only by evil/good-aligned characters. (LIST!!)
From here and here
(modified to only include spell changes)
Animal Summoning II now can bring up to 6 animals instead of 1, 2 or 3 animals in BG1&2EE.
Animal Summoning III ow can bring up to 4 animals instead of 2 or 3 animals in BG1&2EE.
Magic Stone deals more damage now: 3d4 points instead of 1d4 points of crushing damage. Also in IWDEE it deals 6d4 points of crushing damage to instead.
(EDITED) Protection from Evil, among other effects, gives immunity to charm-based spells or effects (e.g. Charm Person, Charm Person or Mammal, Domination, and so on) while in BG1&2EE it’s not the case.
The duration of Remove Fear is changed from 1 hour to 1 turn.
The duration of Sanctuary is also changed: instead of 1 turn it lasts only 2 rounds + 1 round/level, i.e. very shortly in the beginning of the game.
Chant in IWDEE, among other effects, reduces damage dice for all effects outside a weapon’s base damage by 1 (so that a 6d6 fireball will do 6d5 damage, and a flaming long sword that deals 1d8+2 slashing plus 1d3 fire damage will deal 1d8+2 slashing plus 1d2 fire damage instead). The priest’s enemies suffer from the opposite effects.
Also, this spell now has a downside: the priest cannot cast any spells for the chant’s duration, and her movement is slowed by half.
Charm Person/Mammal doesn’t have a +3 penalty to a Saving Throw now.
Hold Person now has the duration of 2 rounds/level instead of 1 turn.
Know Alignment (if someone is interested) now is not Instant, it lasts for 1 turn.
Silence in IWDEE is less effective: the spell no longer has a -5 bonus to a Saving Throw.
Slow Poison now not only cures poison but also cures intoxication.
Also, this spell is not available to druids now (but the druids get Poison immunity at the 9th level).
Call Lightning now has the duration of 1 round/level (capped at 11 rounds) instead of 1 turn/level.
Cure Disease now additionally restores 5 HPs.
Dispel Magic now removes magically created items. The description no longer states the spell doesn’t affect spell protections such as Spell Turning and Spell Deflection.
Also, the description no longer states the chance of the dispel succeeding is determined by the level of the caster and the level of the magic being dispelled.
Glyph of Warding in IWDEE is more effective because a successful Saving Throw vs. Spell doesn’t let to escape the effects of the glyph – instead, it halves the damage.
Holy Smite and Unholy Blight, instead, are less effective: now they give 1d6 magic damage for every 2 levels of the caster, and not for every level, also they’re capped at a maximum of 5d6 at level 10.
Protection from Fire now lasts 1 turn/level instead of 3 rounds + 1 round/level.
Animate Dead now summons not one skeleton that improves with levels, but 1d6 skeletons or zombie.
Also, I would like to mention that the overall summoning limit in IWDEE is 6, not 5, creatures simultaneously.
Rigid Thinking now has the duration of 1 round/level instead of 1 turn.
Strength of One now lasts 7 rounds instead of 1 turn.
Mass Cure is now called “Mass Cure Light Wounds”.
Entangle has no longer +3 to save penalty.
Sunray works differently: it lasts for 4 rounds, it is only usable by druids, and it doesn't have a chance of outright destroying undead
Goodberry heals 5 health/use but you only get 1 item when it is cast.
There're now spells that can be cast only by evil/good-aligned characters. (LIST!!)