I'm still struggling with why it's such a bad idea to have traits that allow for normal units to cast fireball every 3 turns, or heal every 2 turns, etc. I can see it quickly being overpowered, but, as you say, if there's a good system in which those plusses are balanced by thought provoking minuses (cannot wear armor or wield weapons other than dagger or staff if casting spell, plus initiative comes with minuses to dodge, etc), then I think the custom designed units is a great asset to the game, it's just not particularly well implemented currently in a way that screams differentiation and strategic choice.
It seems that would be kind of contra productive since thats what henchmen are for which are unique to the kingdom of Altar and that is what the OP (and lots of others how posted) wish to see for all factions.
All in all I am not realy sure where I stand on this issue. I made the mistake of rolling Tarth beastlords the first few games and while their tactical boni (+ 3 init and attack for army size <4) is nice in the very early game, their items(masterwork chainmail and strongest bows) are mid-/late-game but their stratigic bonus of not having any movement penelties (forest, hills, even rivers) combined with the beastlords ability to charm units multiple lvls above the sovreings invites to rush things. So basicly after 125 turns a challanging, epic game on a large map is done (I control 30% of the map, all empires exterminated and at least twice the power rating of the 2nd place kingdom).
The first game I picked another faction and profession I was actually annoyed because the game suddenly became very slow paced compared to what I had become used to (takes twice as long to scout and lvl your sovreign because of movement, settlements have to build units and not lvl 10 ones by turn 50-75 like the beasts I used to tame not to mention that I actualy needed military research beside mounted warfare). Around turn 90-100 I had build my first hentchmen and not even sacked a single enemy city.
So imo the factions seem to be quite differant considering the overall gameplay but their boni are hard to compare because while some have huge tactical ones (hentchmen -> a healer and/or mage in every army or +25% accuracy -> basic hit chance of 90%+for all units) others have strategic ones. While I realise that those that have only minor tactical boni end up building the same units resulting in being nearly identical in combat I am not sure if that is reason enough to ask for tactical specilization/unique units for each faction.
Giving Tarth a Treant as a counterpart for Golems and Juggernauts would imho make the factions even more simular since everyone shows up with his one slow giant tank unit maybe with a different focus on Armor, HP or dodge but basicly they all do the same job. On the other hand, if you go for real specilization you might end up loosing flexibility since a faction gets unique units, items, buildings, tech and boni and to make them all work together leaves you with limited options -> while each faction plays different from the others it plays the same in every game. (replayability = #of factions, like in HoM&M)