Let's start with profession perks
With the exception of the red-headed stepchild of crafting professions, engineering (which is too "fun" to have real quantifiable advantages), all crafting professions' itemization perks used to be balanced. They all had different ways of getting the itemization and increased power to their players, but the total amount of a power increase you get for leveling any two professions was always about the same.
Now that the best gems you can put into your gear are a little better than they were when the profession perks were being balanced, the perks are no longer balanced. While the jewelcrafter-only gems were indeed slightly improved during the testing for this patch, that change never made it to the live realms. This means that jewelcrafters with the means to gem all their slots with the new epic gems will not be able to get that advantage for three of their slots, which will be taken by the JC-only cuts. Also, blacksmiths who can afford to use only epic gems have an additional 25% bonus to their profession perk of two additional gem slots. If you happen to be a blacksmith and jewelcrafter already, these unbalanced factors basically cancel each other out.
The last time something like this happened was in the end of The Burning Crusade, when all serious competitive guilds were forcing everyone to roll leatherworking to take advantage of a badly designed Drums of Battle. Blizzard eventually limited the level effect of the haste boost in order to prevent serious guilds from dictating the profession choices of their raiders in the next expansion.
It's not as bad as all that, though. These particular nerfs and buffs won't really affect anyone who doesn't have epics in all slots. We all know that you have to be pretty right to have that.
Epic versus rare
Blizzard has said that it wants these gems to feel epic and rare. This is how heroic and 2,200-Arena-rating gear feels, simply because it's so rare and indicates that the person wearing it probably had to display some serious skill to earn it. Spectral Tigers, monocles, and motorcycles don't feel epic. They feel quirky and whimsical, even though they're very rare. Something that costs gold can not be considered epic. Gold can be bought through the TCG loot cards and cubs, and it can be acquired by people with skills completely unrelated to the skills needed to earn epic gems. At best, this means epic gems will be rare, but that won't make them feel epic.
It will, however, make an entire class of skilled players who choose to avoid the in-game economy wish that they hadn't. In order for gladiators and raiders in world-first guilds to not be at a handicap compared to their competition, they have to find a way to acquire enough gold to buy epic gems for all their mains' gear. Scarcity simply drives the ultra-competitive players away from a competition of skill and toward a competition of epic gem acquisition.
PvPers are already a pretty competitive bunch, willing to go to some pretty extreme lengths to get a leg up. The difference between a 2,800 and a 2,600 RBG or 3s team could very well come down to the lost itemization from not having epic gems, if all other factors are equal. PvPers are able to buy PvP-flavored cut epic gems with conquest points, but until they have everything else that they can buy with conquest, the only way they can get epic gems is to raid (a lot) or convince a lot of people who raid or earn conquest points to give them their gems.
Right now, you need to buy about one and a half Guardian Cubs (on average) to get a epic red gem (on average). Also, not all PvPers want to use resilience or spell pen as a stat in their gems. Many gems you will find socketed into the gear of gladiators are actually red (core stats), and those are not available through conquest.
Scarcity is not balance
Raw epic gems currently only come from raiding normal modes or heroics. The Raid Finder does not award anything, and PvP only awards unpopular cuts. Now if all raiders were rational, they'd evaluate the value of the gems they get, compare that to the cost of, for example, a valor-bought BoE, and probably sell more gems than they keep as desperate competitive raiders and PvPers buy them for astronomical sums of gold. At least for the first few months.
Of course, raiders are like most people: They're not rational about money. It doesn't matter that cutting and socketing a gem costs what they could have sold it for, because they have it in their bags and they can use it. They'll trade it for one they need from someone in their group and have a friend cut it. Until the irrational majority gets their gear to the point where they would rather sell gems, competitive PvPers and raiders will have to pay rational raiders hand over fist for raw epic gems.
To be honest, casual raiders are the middle class of WoW, and they're the ones who pay keep the lights on in the Blizzard data center. This is likely the reason Blizzard designed this system this way. Jewelcrafters make tons of gold from the middle class, and this design is a clear attempt to turn the tables and have average players making gold off jewelcrafters.
Here's the thing, though. There are many ways that epic gems could have been designed that would keep the middle class as the center of supply without relying on the whole concept of balancing around scarcity. Right now, as gems become less and less scarce over time, JC will become less and less of a good profession and BS will become better and better.
Instead of balancing around scarcity and assuming that "most people won't be able to get epics in all their sockets" (while rewarding those who can with faster progression and higher Arena ratings), they could balance around the assumption that eventually, most players will have most sockets decked out with epic gems. This would require blacksmith sockets to only take the old gems, and increasing the stats on all the JC-only gems in order to balance the trade skills, and implementing some additional sources of raw gems like transmutes or a higher drop chance in raiding.
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