I have to make one HUGE request: bring back the mod directories. The idea of modular modding is great and all, so leave it in. But why oh why had the mod-directory to go? For Total Conversions it is so much easier to have an isolated xml base.
Just look over at Civ5 - it is such a mess and work to disable all the stuff that's in there to setup a blank modding base to get you going.
So overall it would ease the creation of TCs and also would make it easy to create Mod-Mods.
EDIT: actually I've some more requests:
1. I want to be able to define item categories and set how much of it a unit (be it hero, soldier-unit, creature or whatever) can wear. For example: Definition of item category: Backpack. Then max number of Backpacks worn on all units: 1
2. I also would love to be able to define unit categories and also items that grant item categories. So for example: Humans start with unit category "Human". If the players equips his human soldiers with bows they receive unit category "Archer". Should thy also get a horse to ride on they also become "Cavalry". All those Categories are linked together. Now we can also define Weapon/Attack/Spellboni against certain unit categories. Please allow boolean logic. Like Damage Bonus against: "Cavalry" OR "Archer" NOT "Dwarf"
3. Provide support for moddable talent/promotion-trees (comparable with Diablo2+, AOW, Civ4+) also not just for heros, but make it possible for the modder to add it the every creature he likes it to. Also grant the possibility that certain Items grant access to skill-trees when worn. For example: the holy medal of Empire grants the access to the skill tree: "Empires Choosen", or for example the Thief-Hero Kazilian starts with access to the Rogue-Skilltree. The normal stats should either be able to be auto-leveled or disabled altogether. Of course if the modder so wish he can still use the old stat system as it is now or link it like: Skill "Dodge" needs a minimum Level of 4 and minimum Dexterity of 19. Just as an example.
4. Ability-Effect Triggers. We need special triggers to call spell/ability effects. The ones I have in mind are: On attack (attack-animation is sufficient as trigger), On hit sth (you have to attack and actually hit it, but it's not necessary to damage the target), On damage sth (you have to attack and damage the target to trigger), being attacked (you have to be target by an enemy, you don't have be hit at all), beeing hit, beeing damaged
5. Ability and Spellchargers: please add forms of charges. Like ability "Mighty Blow" can be used 4x times a battle. Or "Battle Cry" can used without limit but with a 3 battle rounds cooldown. Also let certain abilities / spells cost resources. Like for example "Rune-Shaping" costs 4 Metal to use.