Here I won't talk about skills or any existing issues. I want to suggest one big idea for monster sub-classes.
But first let me to explain my logic. How monsters differ from animals (including humanoids)? Usually we refer to monsters as unnatural creatures altered by magic. And the exact difference is in their bodies becoming related to the elements or any other phenomenon, so they acquire it's power, benefits and disadvantages. As you may know, physical appearence of a creature (in TES) expressed in it's life energy (we call it health or HP). For the animals there is no need to have an extra life energy, because they already have enough to live, but for the monsters with their extra energy consumption they definitely require more just to sustain their unnatural existence.
With all said above I suggest to make monster sub-classes dependent on their health resource (HP bar). In my opinion it may resolve the main problem: they won't be overly strong by having magicka or stamina skills in their arsenal because of different main resource. Speaking of the last, player will be able to mix his characteristics to achive the level of balance he want.
P.S. By doing that we also may throw away the debuffs like "Increasing Regular Ability Costs" and make transformations as long as the player can sustain his health resource (but it's the matter of discussion).
What are your thoughts on this?