Considering Transformation itself - I know that its actual effects are unmoddable as for now. But making it earlier and cheaper (And I also meant not requiring Nature 5 here) could be enough to provide Nature with adequate thugs. At the same time, transforming mage into a definite form is a thing which I consider to be both thematic and useful - so, until somebody comes with a way to mod it (I seem to remember someone making a code-digging for additional spell effects...) just consider it a lobbying for future inclusion of such possibility (of course, it's also possible to use a feature of summoning new unit while killing the caster - but this isn't the same).
To JimMorrison:
By Salamander I meant more of an alchemical Fire spirit than either DD or Abyssia version (DD one isn't that bad as a starter, though - just not very thematic. But then, it could be quite similar to already mentioned servant to Magma King).
As for SC killing I don't think that Fire is where we should look for it: a self-evident feature of fire creatures is either fiery attack or defensive fire (fire shield or heat aura). Any SC aimed to fight your armies and mages when you are known to have Fire is pretty sure to be immune to it. Of course, there is a possibility to use either Banefire or Acid as attack type - but you say that you don't want cross-path summons here... The only thing remotely close to Fire which could be effective against enemy SCs is making it a being glowing so brightly that attacking it could inflict blindness - on the other hand, we already have this in various angel-types...
Considering Air I think that it just shouldn't duplicate other paths, but concentrate on what it does best. And this points us to flying, glamour, missiles - and generally, to raiding. At the same time I think just making Great Eagle-type commander is useless: misc slots only it can't be made into an SC or strong thug and even with Air magic it would remain weak - useable as a commander of flying troops but not on its own... I seem to remember, though, that there is a depicting of astrological sign of December making it look like a centaur with wings. I don't remember how it's called offhand, but it may be a base for Air thug also... Still another variant is a Draconian mage (though lack of hands makes him not so usable as thug).
As for Hellboy - I don't like 4-color comicses, so I don't think I will ever see it. ON the other hand the idea itself is both old and viable.
And Ushabti I think isn't so specific an idea - sacred statues which suddenly come to life appear in many places...
On jellyfish - yes, precisely.
I remember such beauties from the old game Wizardry 7: Crusaders of the Dark Savant. Actually, I think that playing it again may be useful just for picking up some interesting monsters...
Shadow Seers - yes, name escaped me, but I think that building on what is already in the game makes it more easy to fit thematically. And they are cool as described...
Considering snake - well, "it never helps", but I just couldn't help it.
ON the other hand, if it gets the poison like that of The Fang it can be pretty effective against SCs especially. Army may stomp it, of course - but this would also depend on which other features are implemented - armies seem to have not-so-easy time with Wyrm...
As for Death - even in Enchantment, it already has both Lichcraft and Buried in Ice/Sand, which, while pricey, are very good thugs, bring troops and may add to magic diversity.
I really don't see what may be added to it... But wait, there's more! (c) Baalz. Death allows you to bring dead hero back as a mummy!
Blood may use something non-unique which isn't Vampire, though (as much as I like them, they are already in the game and doing quite well). A possibility that I see is something like a champion of Demon Knights. There are also many variable demons and Horrors, though most of them are quite specific, so should be nation-restricted...
There was a good thought about human heroes in Aezeal's post, too, even though it seems to go beyond the scope of this mod. (Cerberus is a good beast, but it is as correctly stated unique - and nation-restricted, too!) Inicorn, though, could be used even independent of rider - some authors even make them shapeshifters (though I don't remember tham as such in actual folklore)!