Hero differentiation I think is one of those areas where you can just keep improving it forever, it can only get better the more you work at it. But you also do not want it to become too complex, because it makes the RPG part of the game overshadow the 4X part. The balance between different things is as important as the parts themselves.

One thing that is bad about it, is that in 0.86 most heroes are "blank slates", their only real defining characteristics are what spelltraits they have. The other traits are generally available from level-ups. Therefore, I think, heroes should be given fairly unique traits that you can't find anywhere else. Like, perhaps a hero hates the Tarth faction and will not fight for them, and gains 20% damage against them (maybe if you ally with them, the hero becomes immobilized and refuses to fight for you). 

There are some improvements to look forward to from what I've read of the plans, but I think that champions should be famous (i.e. have a reputation) and have a unique appearance. It adds to the world immersion when characters have a background.

Maybe they should all be on customised mounts so that they stand out more? There is much that could be done, and done quite cheaply too I would venture.

Maybe a few should not even be able to ride a mount, but get other bonuses instead (to compensate)

Anyways, I don't think we can really go wrong in the realm of champion differentiation. If they are all blank slates, they are completely customizable ... and if they have ENORMOUS branching trait trees, I really don't think more complexity in trait decisions can ever go wrong in this one particular instance (as long as we only have a few choices at each particular junction, but they take us down a specific path-set based upon our class, and our early decisions.

Also, going the other way, if they all already start with their own Class, legacy, unique spells, unique abilities, and we can only choose between a few path-sets (He is Zealot Warrior of Aragon, you can choose either Divine Crusader, Soldier of Light, or Rage of God (Bezerker type) subclasses ... and each would have a modicum of branching trait paths.

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examples

Zealot of Aragon -> Divine Crusader, Soldier of Light, Rage of God

Warrior of the North -> Blood Bezerker, Soldier of Ice, Barbarian Lord

Barbarian -> Blood Bezerker, Conqueror, Barbarian Lord

Eastern Dervish -> Sand Bezerker, Soldier of Stone, Prince of Thieves

Halfling of the Hills -> Soldier of Stone, Soldier of Light, Prince of Thieves

Gared the Rogueling -> Prince of Thieves, Master Assassin, Bow Master

Frank the Archer -> Bow Master, Soldier of Wind, Flurry Artist

Assassin of the East -> Blade Master, Shadow Arts (assassin/mage combo class with shadow magic and ninjutsu abilities), Master Assassin

Assassin of the South -> Fire Dancer (acrobat/mage combo with free weapon enchantments), Bandit Lord, Master Assassin

Assassin of the West -> Marksman, Master Assassin, Shadow Dancer (assassin/acrobat combo with stealth abilities)

Sharpshooter -> Marksman (better criticals with ranged, higher crit chance), Bow Master(stronger range attacks, various types of "arrow" abilities"), Elite Sharpshooter (100% accuracy w/ ranged ... chances to ignore all armor)

I like the vein in which Tasunke is thinking there. Anything along those lines that gives a champion a particular skillset and title goes much better for RP and story.

The pool of traits that UmbralAngel suggested and the heirloom feature that Heavenfall mentioned would go hand in hand, but I don't like the idea of randomisation of them for the champions, as then you do end up looking at your heroes as containers rather than characters.

At the moment, when a champion levels up, you choose the stats to increase. Further, they share your sovereign's spell knowledge in accordance with their intelligence. Add to this the fact that they draw on your sovereign's mana reserves, and you see that champions in WoM and FE are truly just indistinct containers.

Sometimes less control is a good thing. In MoM, the abilities and statistic increases per level were pre-determined, and this made certain that each hero had their own particular flavour, and forced the player to choose which ones to keep and which ones to reject depending on the game strategy.

For these reasons, rather than suggesting the scrapping or tweaking of all current champion related mechanics, I have come up with a new unit type called Legendaries. A Legendary is a channeler without the ambition to rule a kingdom. They don't need to be imbued, and the ones that use magic have their own substantial mana pools, one for combat which is reset after each battle, and one for overland spells which is reset each turn. Magic using Legendaries specialise in one or two types of magic, and their spells in those schools have considerably higher potency.

A Legendary's statistics and abilities per level are pre-determined. Each has a unique appearance, a uniquely customised mount, and a particular irremovable item which could be a weapon or another item type. All armour and clothing you equip them with takes on the shape of whatever they are wearing, such that their appearance never changes. This distinguishes them from all other units, and makes them memorable.

There should be a finite number of Legendaries, and they cannot be traded. They should be considerably more powerful than any other champion of the same level. Each has a title and a unique set of abilities that they gain as they level up. A good backstory for each Legendary would also be good, but not entirely necessary, as players can fill that blank in their minds.

Prestige should probably be a factor in having a Legendary champion your cause, as well as perhaps faction alignment.

Some Legendaries will have inherent magical ranged attacks, some will be strictly melee, some strictly archers, some might be flying, others water walkers, etc.

You cannot marry a Legendary.

Lastly, customised voices would really help them stand out, and would make playing more immersive.