Monsters in 3rd edition are arbitrary, like every other edition of D&D, be it 1st, 2nd or 4th. Especially the high-level ones, like fiendish outsiders, who had good BAB, good saves, good hitpoints, spells, spell-like abilities, natural armour, Damage Reduction against all except one type of damage, and so on.
I think you rather mean 'mundane' creatures like orks, goblins and others who aren't that different from humans in terms of magical abilities.
Yes, I sometimes have the impression this is missed or lost.
A humanoid monster that you might be able to play doesn't get much specials. So, basically only Giants and Humanoids have this features. Once you enter the area of Monstrous Humanoids, Constructs, Magical Beasts, Undead, Fey, Outsiders or Dragons, the monsters get arbitrary abilities (Spell-Like Abilities, Supernatural Abilities, Extraordinary Abilities. Fast Healing, Regeneration, Breath Weapon, Constrict, Poison, Damage Reduction).
They are still supposed to be balanced according to their CR, but ultimiately they get abilities players will _never_ get. Sure, you can try to come up with a Level Adjustment, but... If the concept had existed before 3E, it could be applied to AD&D, or OD&D, too.
I am pretty certain that there are players that think that what a monster or NPC can do, I could do, too, with the right training. I was one of these players.

But... I don't think this is necessary. Sometimes its enough to say: Yes, your character can take this training, but then he'd be an NPC.