Scaling is the way it is because at the time the developers did not have time to finalize all classes, and hunter was among one of them.
Hunters using mana, for example, is a consequence of that, as mana is meant to balance classes that can spam attacks or spells like casters yet everything a hunter does has a cooldown. They were meant to use focus but ran out of time.
Otherwise, I agree. They have to shift passive permanent damage to active damage for pets and the BM spec in particular not only so that the game is healthier but also because it’s boring being an auto-shot bot that uses multi shot every 10s.
I wrote a thread providing feedback and ideas that could help fixing the awful state of hunter runes, should you be interested: Feedback: shift passive damage from BM runes to active damage to balance pets - #5 by Zerezas-wild-growth