My favorite part of MoM was how heavily non-combat magic could be used. I'd really like to see E:WoM take that concept much further, especially with terrain modification (real and illusory) and spells that can rapidly dissolve a much more powerful stack's advantage.
Chaotic Mists - Covers a small section of the map in mist for some number of turns. Any stack of units entering the mist loses all remaining movement and emerges in a random direction. (Could be used to temporarily block a choke-point, but not reliably)
Guardian Mists - More powerful version of the above. Affects only hostile factions and always returns them to the same side from which they entered. Also hides friendly units that are within it. (Much more costly, but more reliable and offering perfect cover for an ambush, particularly if a friendly army is teleported into it while the enemy is waiting for it to dissipate.)
Water Walking - Lets a stack move across water for a number of turns. Units on water when the spell ends drown. (I'm a bit surprised it hasn't been mentioned yet. Could be an extremely powerful strategic spell depending on how it is used. Could also have a unit-only, permanent enchantment version.)
Nature Attunement - Similar to Water Walking but increases movement speed through grasslands, forests, and the like.
Earth to Mud - Transforms a small region of land into swampland for a number of turns, restricting movement speed for units passing through it. (Another strategic spell suited to choke-points, could be limited to Empires)
Dire Swamp - More powerful version of Earth to Mud, affects a larger area, completely prevents movement by cavalry and siege equipment, and inflicts damage/debuffs via disease to units passing through it. (Definitely an Empire-oriented spell, could be used offensively as much as defensively, ie slow and weaken reinforcements heading towards your target)
Tremors - Causes small quakes, dealing minor damage to affected units and possibly damaging or destroying structures.
Grand Quake - Causes major damage to units and structures in range, randomly modifies terrain (just up or down a little bit), and can cause impassable fissures. (Major spell, possibly essence-based. Could severely weaken an enemy faction if cast in the middle of a heavily populated area as a prelude to invasion.)
Desiccate - Permanently turns an area into barren wasteland. Units in affected area take minor damage. (Another Empire-oriented spell, primarily used to remove restrictive terrain like forests and jungles. Could also attempt to negate the mist spells.)
Gaia's Mantle - Produces impassable earthen walls around a town or across a stretch of land for a number of turns. (Kingdom-oriented spell similar to Earth to Mud. More potent, but shorter duration.)
Gaia's Rebuke - Tremendously slows hostile units in a large area and causes damage with every movement and turn therein. Also randomly converts affected land to grassland, forest, jungle, etc. in a patchwork fashion. (Think earth and nature actively hindering the enemy; stone spikes erupting from the ground, thorned and poisonous plants growing at incredible rates, etc. More or less a Kingdom-oriented version of Dire Swamp. Could be used similarly.)
Rise of Qin's Army - Creates a number of "Clay Soldier" units at the targeted location equal to the number of all humanoid units (friendly, hostile, or neutral) killed in the previous turn. Clay Soldiers are immune to all status effects, buffs, and debuffs, are unaffected by morale or leadership bonuses (assuming such exist), and are immune to armor/resistance-piercing effects, but cannot be healed. Clay Soldiers cause severe morale damage (again, if it exists) to opposing forces in battle. Clay Soldiers lose one fourth of their initial stats each turn, any units remaining vanishing after the fourth turn from their creation (meaning they go 100%-75%-50%-25%-vanish). (An epic, essence-costing spell only suitable to situations of total dominance or extreme desperation. Empire-oriented since it involves binding the souls of the recently deceased into clay vessels. The degradation could also be thirds to decrease the near game-breaking power the spell would have if used properly.)
Those are just a few that came to mind quickly. I'll see about jotting down some more tomorrow.