As I've already said, I support this idea.
Militant players should get militant heroes. Players using culture, diplomacy, trade, or espionage should get heroes in those veins. What about city mayors, gaining abilities as the city expands/produces/some other measure?
I've also advocated a Court or Council, where heroes have the option of providing Empire bonuses rather than be directly on the board. One of the big moments in Civ4 for me was deciding whether my general took control of a unit, produced their unique structure, or became a trainer for 'normal' units; I'd expect E:WoM to be no less stressful.
I would like, in short, for every possible Victory Condition have heroes that encourage it.
And certain cross-bred heroes. Maybe I'm not the best archer or sword hero, but LOOK, I can do both! Or that halfling hero from MoM, who wasn't the best fighter, but reduced anger/discontent/cultural hostility in the cities she conquered?
One of the best things in MOO2's hero system was exactly the balance Wintersong was talking about. Maybe that archer isn't the best, but if they bring technology with them? What about scouts or merchants bringing maps, or spies that already have enemy secrets? Or heroes like Warcraft's Priestess of Elune - not the most damaging herself, but made the archers around her that much more deadly. (None of which makes her 'ultimate' ability any less deadly. )
Consider the pen & paper RPG Ars Magica: There were times when you wanted to take your second or third best hero, because your 'Alpha' hero was making an item or conducting a ritual. Yet you still had levels of experience among the hired help, or minions.
Oh My. Just an idle thought - what if certain advantages are ONLY acquired in combat? For example, only units confronted with Fear become truly Fearless instead of Brave (which can be trained). Only units that fight undead become Deathslayers, skilled at dispatching the mindless minions of your annoying Lich neighbor. I can see several BANE skills, each one gained ONLY by actually going out and killing. And it encourages variety in the enemy armies - Do I really want to send summoned elementals out after a unit that just became better at killing them, or do I suffer the hundreds of infantry deaths instead? Are too many of the enemy units resistant to my fire spells, forcing me to change magical tactics? It just adds another level of awesome to combat experience.