Hunters don't like running out of mana in the middle of a fight, but other mana users don't like that either. Are hunters entitled to something like rage or energy as physical damage dealers like warriors and rogues, or are we just being picky? Since we aren't really wizards of any sort, does our use of mana cause more problems than it solves?
One thing to keep in mind is that intellect helps out casters a lot by providing spell crit in addition to mana pool, whereas for hunters it only provides a larger mana pool, often at the expense of physical crit. My wild brainstorming mind imagines: what if hunters had a "focus pool" much like mana, except that it was determined by agility rather than intellect? This way, it would let us focus in on fewer important stats which benefit us in more ways than one. On the other hand, perhaps having to juggle more stats than usual is one of the things that makes choosing hunter gear a more interesting task.
This is a big problem on lots of hunters' minds -- but what's Blizzard going to do about it? It's been a problem since the very beginning, and so far Blizzard's main answer has been Aspect of the Viper. Whether that is enough or not remains to be proven. Wrath of the Lich King may bring more mana-regenerating abilities, but personally I would prefer an overhaul of the mana system, and a replacement with something more hunter-like. Call it focus or energy, pizzazz or chutzpah; it doesn't matter to me, but make it feel more like something a hunter would use, not a magician.
The idea behind learning new pet skills out in the wild and then gradually teaching them to your pet is a great one on the surface. The first time you're leveling a hunter it can even be quite interesting to go hunt down the pet skills you can get as they become available. But once its novelty wears off, it becomes a mere chore, especially if you're leveling a hunter for the second time, your heart yearns for something more efficient.
To make things worse, the current system requires that you always keep one space available in your stable for switching out with various throwaway pets, tamed only for the abilities they have to offer your regular animal companions. From an endgame perspective, when people like to have maximum versatility for various situations, the current implementation lacks in elegance as well as efficiency.
We will probably see Blizzard introduce some solution intended to simplify this at some point. If they do it right, they'll likely use a reductionist method to just try and blend it in with other elements of the game. If not, I fear they might try to introduce some entirely new mechanic that just shifts the problem around without actually solving it. We'll have to wait and see.
Pet abilities and versatility
Mania's Arcania recently did an awesome review of the pet versatility problem. Hunters want each species of tamable beast to have its own different pros and cons, each one viable in its own way for various situations. In our wildest dreams, each pet would be like its own little mini-class we could attach to our hunter for a unique hunting experience. From a design perspective, however, designing and balancing all these abilities just for one class could seem like a major commitment to which Blizzard just doesn't have the time and energy to devote.
While I'd settle for Mania's suggestions on a good middle ground, I can't stop dreaming of a future in which hunters really have an awesome array of pets to choose from, as well as an awesome arsenal of tools (from pet gear to pet talents and abilities) they can use to customize those pets to their liking. I tend to think Blizzard is still holding out for that one great day when all pets can really start living up to the vision they originally had in mind, and I'd be surprised if they actually give up on that dream and settle on some sort of compromise. It's much more likely that they'll either go ahead and do pets right at last, or else, sadly, let them lag behind indefinitely, forever awaiting their chance to shine and never really getting there. I know Blizzard's full of creative people, and as a creative person myself, I know how it is when you've got this great project you really really want to get to someday, only to eventually lament that "someday" never came.
This is one problem Blizzard is having across the board with all the classes: they've created so many different talent setups that take advantage of so many different combinations of stats that players are having a hard time finding the right mix of items that match their talent build of choice. It's an even bigger issue for hybrids like druids and paladins, but non-Beast Master hunters are having trouble getting gear that appeals exactly to their nature as well.
I think we will see that Blizzard's solution to this is an evening out of the kind of gear required by any particular specialization within any particular class. Just in the same way that some feral druid talents were changed a while back so that cat druids could make better use of the same gear that rogues use, we will see Blizzard making all hunters use more or less the same gear. Items will either be "for hunters" or "not for hunters" -- but then again, it might turn out to be "for hunters and enhancement shamans" instead of just hunters. I don't know enough about enhancement shamans to be sure.
We've covered line of sight in PvP before, and it's still as much of an issue as ever. In addition to that, many hunters complain that their pets die way too easily in PvP (and raiding) situations, and wish that more of their stats carried over to the pet, most notably resilience and armor scaling.
Blizzard may very well buff pets up a bit -- that seems easy enough to do -- but the line of sight problem is much more perplexing. Personally I'd like to see hunters get a long casting time heat-seeking missile of some sort in the expansion -- with a knockback effect for kicks -- just for situations where people are hiding behind pillars.
Talent trees and specific abilities
Many people seem to think that Beast Mastery is just fine, but that Marksmanship and Survival are having issues. Some of the talents seem lackluster and less synergetic than Beast Mastery talents. Likewise, when it comes to more generalized specific abilities, there are many varied points of view. Some people say that traps are not useful enough, for instance, or that their cooldown is too short. Others say that Beast Lore, Tranquilizing Shot, and others should be changed so that we use them more often.
Specific abilities like these are the hardest to predict. Blizzard has their own mind when it comes to tweaking things. I have yet to see any player suggest "Ability X should be adjusted like such and such" and hear Blizzard respond, "okay!" More often they look at the general principles we raise and then apply their own solution to them in a way we'd never have thought of on our own.
Blizzard's unpredictability applies for every issue on this list. We can tell them the problem and ask them our questions, but the answer we get will almost never be what we expected.