In vanilla, no one would have been surprised to learn that Blizzard designed hunters last. They had a mishmash of ranged and melee abilities, since Blizzard couldn’t quite decide whether they wanted melee hunters to be a thing. The Survival tree retained remnants of the melee hunter concept and was quite a mess at launch. The 8-yard “dead zone” that prevented using a ranged weapon against melee-range enemies was another remnant of the melee design — and endured for quite a long time. The stacks and stacks of consumable ammo to lug around lasted even longer. The pet feeding/happiness mechanic was cute but kind of a drag. My vote for the biggest problem with the vanilla hunter class as a whole, however, was mana.
Mana made very little sense for the hunter class thematically or mechanically. Aside from Arcane Shot, hunter abilities were not particularly magical in flavor. Even in Azeroth, your ability to fire a bow or a gun has nothing to do with harnessing magical energy: both warriors and rogues managed to use these weapons just fine without a blue bar. The argument of course was that hunters did special things with these weapons that set them apart, things that required mana to pull off. But it just never felt right. And it led to bizarre itemization at times, such as the hunter set from the Temple of Ahn’Qiraj which originally included bonus spell power.
The class hadn’t been designed for a mana system. Believe it or not, the Focus system that Blizzard eventually implemented in Cataclysm was an evolved form of what the class had in beta. Beta testing proved that the system was too powerful compared to other classes, and with a lack of better last-minute options, Blizzard opted to staple on the preexisting mana system.
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The problem was that hunters had no good way to regain mana once they burned through it. Raiding hunters found themselves chain-chuggging mana pots so they could keep up their DPS. Sometimes they would use Feign Death to get out of combat and drink. They could also use Viper Sting against targets with mana, but the vanilla debuff cap prevented this from being a viable option in most circumstances. Blizzard eventually gave hunters Aspect of the Viper, which went through several different forms until it finally allowed you to regen a percent of your mana pool with every hit. However, the mana regen came at the cost of dealing 50% less damage plus taking you out of an aspect that buffed your damage — a double whammy. Even with this new aspect, the class had mana issues deep into The Burning Crusade.
Much to hunters’ chagrin, the mana system persisted into Wrath. Finally, with the Shattering in patch 4.0.1, hunters switched over to the Focus system and became the class that Blizzard originally conceived.