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Improved Invisibility + SI: Divination makes them impossible to target with breach, and my mages are too low level for dispel magic to do anything.
Furthermore, they seem to have ridiculous ACs: Korgan (with a THAC0 of 3) is missing on a 17! Melee enemies certainly don't have armor that effective.
The mages are intelligent in that they will react to the spells you have cast or have casted. This means that you can fake them out using decoys. Say, if you need to prevent them from removing your party's magic, send only one person in with spell protections and have the enemy mage remove that one person's spell protections.
The real dangers from mages are the AoE spells that disable or damage like Dragon's Breath or Horrid.
SPOILER!They won't cast it on a person protected from magic damage, so what you do is you send in someone not protected by it with high hp, then you send in another melee guy that is protected. The mage casts Horrid and damages your first guy, so withdraw that person from battle, heal him up, while taking the mage's attention with the second character, which is hopefully meleeing the mage and getting spell disruptions.
The key items you will need are potions of protection and elemental resistance, or spells that do the same, along with + ac items and Flail of Ages +3. The elemental damage of the flail makes interruption more convenient and if you have Anomen, you have plenty of spells, protections, ac, str, and number of attacks for it.
Some mages you can cast greater malison on and emotion them. Others you can't, because they are immune or have too high spell res.
One primary you will encounter is dealing with melee enemies while dealing with mages. A single mage alone, so long as you have enough spells and hp to take his damage dealing spells without dying, is no threat to you with proper preparation and battle tactics. A mage with a bunch of summons hitting you and all kinds of other high negative AC and high negative THACO will make things much harder.
The way to deal with melee mobs that is hard to hit with 5+ rounds of attack and less than 0 THACO is to use these spells. Malison, Emotion, hold spells, slow, breach (for hardiness HLA), and simple damage dealing spells like missiles and flame arrows.
Here is the suggested party composition for new people to IA, from my view.
Berserker/Mage
Fighter/mage
Fighter/cleric
Sorcerer
Auramaster
Pure Berserker, barbarian, fighter, or Ranger-Archer. Or a second mage like Nalia.
It is better to have dual classes since they can get 3 attacksperround with 5 proficiencies. Or you can use the unnerf multiclass grand mastery thing. Humans have bad saves compared to paladins and dwarfs like Korgan, so if you want a pure fighter, Korgan is probably pretty good since you don't need to obsess over his saves using improved invis or potions.
Here is the basic guide to mages and fighters.
SPOILER!If you see a mage, CTRL+Q him into your party and take look at his resistances with and without spells pros. CTRL+R will remove his spell protections. Figure out which spells you have that can damage him given his spell protections and plan the entire battle beforehand in your head. Reload to before and fight him. Watch the spells he casts, who he casts them at, and wait until you are defeated or victorious. If defeated, use what you have learned to modify spells, tactics, and order of actions. If one spell doesn't work, meaning you see "Casts Emotion" and you don't see "Saves vs spells", then he's probably immune either naturally or through his spell pros. This means time to change tactics and spells.
For fighters, you should lower their resistances/saves and then disable them using enchantment spells or web. Have your fighter/mages cast minor globe or have anomen cast free action on F/Ms and then wade in to slaughter the fighters once they are held.
If fighters are immune to spells, then you will have to use an uber tank like a F/M or even Cernd the Auramaster to take the hits, while using other fighters like Anomen to beat them down. For fighters with high regen, you have to use "every' fighter, preferably with haste on, chant, bless, improved haste, and so forth.
For Fighter/mages like the Greater Yuanti, then you have problems, because now they are fighters plus the mage protections. Unless they are vulnerable to emotion and enchantment. you'll probably have to wait until Chapter 6 to kill em.
To Sikret, I tend to think there should be more hints that there is a powerful enemy waiting around. Once you enter the troll mound, the entrance closes, and the first enemy you see is a weak spirit troll. The hints should be either in the high level mobs that guard the entrance to certain places out in the open like druid's grove or you have a high number of low level mobs defending it.
This will make battle difficulty more intuitive for new players as they don't immediately go from weaklings to the Troll Queen/King thinking they are there to be fought with the Druid grove quest.
This can't be done for all encounters, say Crypt King, but it can be done for the areas which were unusually low level in the vanilla game. The Planar Sphere warning was nice given the new difficulty.