Since adding skills (AFAIK) isn't possible, and the only thing we (well, the GMs) can do is either tweak skills or add new weapons, there might not be much that can really be done. Sure, you can add X weapon or tweak X skill, but then others would complain about it and endless balances might ensue like OP stated.
However, one major issue I have with elves and giants are their transformations. Compared to elves and giants, human trans-be it DK or pally, are complete trash. Paladins for their 'unique" skill get some extra prot (which can be even lower than the prot and/or def they were getting from the title they had on before transforming!), big whoop. DK's get it even worse. Sure-you can get that glorious 180% stat boost at the sacrifice of a 60% stat and all of the passive defense skills always activate (at the sacrifice of lower overall protection from any and all damage sources, along with a lower melee ping rate-20% compared to 30% of the others). Their unique skill is completely useless however. When is the last time you ever saw someone fomor control anything? Never, that's when.
Elves and giants on the other hand get actual useful skills (full swing and magic missle). What I'd like to see is a tweak or buff to Paladins and DKs. Make DK's skill actually useful, like a stat boost to the monster(s) they take over ala lives soul link with pets. That would be INSANELY useful, as DK's are insanely squishy compared to all the others (aside from elves, but they are meant to be more of a glass cannon). As for Paladins, make them tankier, not a ton, but more-so than they are so that they don't actually lose defense by transforming. Their "role" if they really have any, is to protect others and soak up damage. But they can't really do that with the measley 15 def and 6 prot at rank 1.
Any thoughts?
I think it'd be sweet if human transformations could get cool active skills, but since adding skills isn't really possible for now, I don't see it happening. Control of darkness is completely useless, especially since taming mostly makes it obsolete. The skill would have to be replaced completely imo. However, your other points about DK being bad are pretty untrue. Dark knight is the singlebest transformation in the game, and it is human's saving grace.
You can remain in the dark knight transformation indefinitely in the endgame, as you make more than enough money from spamming missions while transformed to sustain the cost of chugging potions to stay transformed. My issue with infinite DK is that it represents too much of the power budget for humans. In the context of lategame/endgame, if not for DK, I'm of the opinion that humans are strictly inferior to elves and giants. Even when transformed, humans fall behind elves in my opinion, although they are likely stronger than an untranformed giant in most aspects. Being infinitely transformed/mashing pots forces a certain playstyle and has some drawbacks as well, such as not being able to use magic (because you have 0 int) and not being able to eat MP pots (unless you are using ranged in DK, because eating MP pots when pot poisoned lowers your strength).
Even though I use infinite trans myself, because it is a powerful tool for humans, I still think it is an "unbalanced" thing, not in that it makes humans too powerful, but mostly that it has too much of human's power budget, like I said. I think the idea of transformation is that you get a significant power increase for a short period of time, and the elf and giant transformations do this very well by having a clear timeframe, and also you get access to a powerful skill during it. Paladin fails to do this as it is lackluster, and not having a trans skill is just indisputably bad compared to elves and giants. Then on the other hand, dark knight is unequivocally better than paladin because you can stay in it infinitely. I could expand more on the topic of transformations but it's a bit beside the point of my thread.