Btw i am MM6 fan too, so count me in.
I am afraid i cannot help with the technical (ERM) advices how to realize the ideas, but i could try to give some ideas about common things.
0. I suggest to increase conception a little bit - not to use strictly MM6 world, but some parts from MM7 and MM8 too (+already start making some things for the future sequels).
1. About mobs which would act as heroes-commanders - lets call them adventures to evade misunderstanding. As i said - i will make defs for them.
1). I just need to know how many of them should be (7 or 14 - both male and female per class) and how they will look like.
2). About weapons - i suggest that class always uses the weapon he most profienced (grandmaster - by MM7-MM8 rules), so knight (weapon) is going with the sword and shield; paladin with 2H hammer (for example); cleric with mace and shield etc. - Thus we'll solve the problem with their appearance - static def for all cases. Of course, this will add less variety to the game, but would be more logical overall.
2. About hero and adventures - i think hero could just work as some "container", which would act as:
- a bagpack with all items (which later could be passed to adventures)
- a "skillbook" with all skills, using of which are common for all adv-res like diplomaty, identifing mobs and items, repair, alchemy, etc.
- a paperdoll for equipping artefacts (like d2 talismans) which would affect the entire party
3. I suggest to create a new system for levelling adv-res with primary stats like strength, dexterity, stamina, etc. (could think about its details in case u would accept it).
Too sad we cannot add more animations in the def... In this case i could make separate animations for melee, bow attack, spellcast and all-around attack.