After playing the mod quite a bit and getting a feel for all the mechanics, I've refined the ideas I had.
Instead of Commander, I think the name Vanguard is much nicer for the changes I've thought up.
Vanguard: Forward shock force.
Diplomacy - For the strong shock force of a Vanguard.
Rune Magic - Defences bonuses and spells to help gain a foothold.
Engineer - Strong forward bases.
Warding - Vanguard are usually the best, which means best protection.
Demolition - Part of being a shock force is destroying as much as possible.
Juggernaut: One man fortress. For people who just don't like dying. Cop out gimmick.
Constitution
Invulnerability
Elemental Resistance
Evasion
Magic Resistance
Dreadnaught: Pure offense. Cop out gimmick.
Weapon Master
Ignore Armor
Ferocity
Mighty Blow
Swiftness
Infiltrator: Force disrupter
Running - Kiting and escaping.
Chaos Magic - Get in and sew the seeds of chaos amongst the enemy forces.
Evasion - Avoiding detection and attack.
Poison Magic - Poisoning a water source can defeat an entire army.
Ritual - A life of espionage is perilous at best. You need to make sure you do everything precisely.
Changes to classes already in-game.
Warlock - Given that warlocks are witches, just male, I think Witch Hunter doesn't make much sense. I don't really get Summoning Magic or Mage King, either. I think changing most of their kit might be a solid go. (Deflection, Chaos Magic, Fire Missile, Mighty Blow, Occultism) That'll give them a nice theme of being something of a battle caster, while allowing players the roleplaying background by choosing races that have Lore, Energy and/or Ritual, since witches/warlocks are supposed to be self-taught. So, it's up to the player how they learn and practice.
Bard - Bardic poverty being a running theme for bards, I feel it would make sense to remove wealth and give them Energy instead. Not sure about Fire Missile for Bard, either. Could go with the Dragon Age style Bard. (Poison Magic, Convincing, Energy, Leadership, Ignore Armor) Perhaps something a little less murderous. ( Convincing, Energy, Leadership, Trade, Diplomacy)
Tinker - While it's great to have a class that offers 2 resources, I feel Quarrying doesn't fit. Stone doesn't seem all the important to any tinkerer I've ever known of. Maybe replace it with Convincing, instead. (Engineer, Trade, Convincing, Smelting, Alchemy)
Necromancer - There's already Lichlord, which Lich's had to kind of be Necromancers to begin with and most of the classes named after a specific magic type in the game are just the magic type, ritual, gate, energy and time magic. I offer the idea of changing Necromancer to Medium and changing Time Magic to Divination Magic. (Necromancy, Divinination, Ritual, Energy, Gate)
Alchemist - Gate doesn't make much sense to me for alchemy, however Wealth does, in that the primary reasons for alchemy is monetary gain. The Phillosopher's stone was even said to have properties that could turn things into gold. (Alchemy, Ritual, Energy, Wealth, Potion Master) Perhaps... and this is my preference... (Alchemy, Quarrying, Smelting, Weath and Gemcutting.)
Sage - Sages are booky, right? Could make them do some class meshing and have them more the role Archmage fills and have Archmage as your Arcane power house. (Illusion, Summoning, Time, Alchemy, Lore)
Paladin - Witch Hunter kind of makes sense in a way, but not really. Paladins wouldn't likely have anything in particular against spell casters, I think and witches aren't necessarily evil. Plus they already have Smite Evil that should encompass any spellcasters they would want to kill. I think they it would make more sense for them to have Leadership. And probably Divitination Magic over Healing. I also view Paladins as valient defenders and tanks, so Constitution makes sense to me over Ferocity. (Leadership, Divination, Knight Protector, Smite Evil, Ferocity/Constitution)
Priest - Warrior Priest/Witch Hunter idea. Sort of purge the wicked thing. (Witch Hunter, Deflection, Pyromancy, Divination Magic, Energy)
Healer - Real-world healers spend all their time tending others, but don't often seem to get sick themselves. This makes sense to me. (Healing Magic, Elcor's Aura, Energy, Regeneration, Warding)
Monk - Monks are generally tranquil. Perhaps Armor Piercing instead of Ferocity. 'Cause they know where to hit or something.
Ranger - I don't get Quarrying and Fire Missile here. Maybe Elemental Defense (they're generally out exposed to the elements?) and maybe Engineer ('Cause they know how to make the most of natural resources?) or Illusion Magic (so they can screw with poachers or something?)
Shaman - Great Shaman's lead and protect their people with runic divination tuned into the energies of the Earth and spirits. (Divintion Magic, Rune magic, Warding, Energy, Leadership)
Archmage - The boss of the magical world. (Occultism, Mage King, Lore, Energy, Time Magic)