I think part of the flaw in the core class system is the misallocation of roles. Going through the talent trees intentions (assuming a perfect world, which I know isn't true, but its the variable I'm controlling for) :
Druid: Spell DPS role, Tank role, Healing Role
Hunter: Ranged DPS role x3
Mage: Spell DPS role x3
Priest: Healing Role x2, Spell DPS Role
Paladin: Healing Role, Melee DPS Role, Tank Role
Shaman: Melee DPS Role, Spell DPS Role, Healing Role
Rogue: Melee DPS Role x3
Warlock: Spell DPS Role x3
Warrior: Melee DPS Role x2, Tank Role
Now to add up all of the total possible roles in a perfect world:
3 Tanking Roles, 3 Physical Ranged DPS Roles, 5 Healing Roles, 8 Melee DPS Roles, 9 Spell DPS Roles.
This says to me that Melee and Spell DPS roles have been very overallocated. This will lead to tension over gear unless specifically school-of-damage itemized, which Melee DPS doesn't really even get the benefit of.
Now in the perfect raid with almost one person from each spec, we can see the intent doesn't match the setup, which I think is the source of the problem. Certain classes like Druid and Shaman have traditionally been "pushed" into healing over any other choice because of the lack of healing roles overall. Hunters, being an 11th hour addition, have the odd position of being the "safe" DPS class and the physical ranged DPS class. Since the game is so spell/melee DPS biased, and people will make guilds/raid based around that expectation, it becomes a little clearer why hunters are swept under the rug unintentionally (except for Mother and the other times they are thrown a bone.)
I think a better solution would be to bring the potential roles to a place where they're in a better equilibrium. With the appearance of the Death Knight, a primary tanking and DPS role, I think Blizzard is on the right track. If things follow in the same productive manner, I think Hero classes could sort things out. If there is an all out Spell DPS focus class, though, I will probably scream
(On another note, I think it isn't wise to have a class like druid or shaman with, ideally, 3 very different, well-performing roles while mage/rogue/warlock are locked into one focus, but I think its far too set at this point. Something drastic like axing the whole stupid rogue tree no one cares about and making them into a viable ranged physical DPS throwing class would be keen though.)