I’ve had this conversation multiple times since I looked up the MoP profression bonuses for my Moonkin guide, so just want to write it down somewhere while I have a moment.
In the past, primary and secondary stats were placed on gems in the same quantity (compare 40 Int with 40 crit). This meant that primary stat gems always dominated all other options (let’s put aside some complication with tanks and various mitigation options). You’d sometimes use other colors to meet a meta requirement or the occasional socket bonus, but you basically made your gem coloring as “red” as possible at all times.
As far as professions were concerned then, a profression which gave you extra gems (Blacksmithing) or upgraded your gems (Jewelcrafting) was equivalent to giving more of your primary stat (since you wouldn’t use them for any other purpose), and could be easily balanced against +primary stat bonuses from other professions.
In MoP, in an effort to make gems more interesting, primary stats (Int/Agi/Str/Stam) are only placed at half value on gems (compare 160 Int to 320 crit). This also applies to hybrid gems. Point being, since half as much of a primary stat is more in line with the value of secondary stats, gem choice is interesting again. Most classes have at least one secondary that they prefer to primary at a 2:1 ratio, in some cases by a wide margin.
What does this do to Blacksmithing and Jewelcrafting? Well, if (continuing the examples from my links), crit is much better for you than half an Int, then you’ll use your blacksmithing bonus to give you 640 crit by socketing two yellow gems, which is somewhat better than the 320 Int you’d get if you used two red gems, which is important since 320 Int is the bonus from most other professions. So Blacksmithing to generally be the most min/maxy choice, by an amount that varies based on how much your class likes its best secondary stat. This is aside from the added flexibility blacksmithing has always offered with haste/hit caps and the like.
Jewelcrafting is trickier. Sticking with the example, you can upgrade a red gem to 320 Int (a gain of 160 over a non-JC gem) or a yellow gem to 480 crit (again, a gain of 160). So wait a moment: using JC to gain a secondary stat is inefficient; you don’t get twice as much of it. So first conclusion: never use non-primary JC gems if you’re a Jewelcrafter. Second point: if you replace two red gems with 320 Int JC gems, your total gain is 320 Int, which appears to be in line with standard professions. However, since in our example crit was the favored gem stat for our class, you won’t be using 160 Int gems to start with, you’ll be using 80Int/160crit gems in red sockets. And replacing two of those with 320 Int JC gems is a smaller benefit.
(Spelling out an example if this isn’t clear to you. Say an Int gives you 1 DPS and a crit gives you 0.7 DPS. Then you’ll be using 320 crit gems in yellow sockets and 160crit/80Int gems in red sockets. A normal profession gives you 320 Int for 320 DPS. Blacksmithing gives you 640 crit for 448 DPS. Jewelcrafting replaces two of the orange gems with 320 Int gems, so in total you lose 320 crit and gain 480 Int, for a gain of only 256 DPS.)
Why this imbalance? I think, simply, there was no easy fix for Blacksmithing and there was for Jewelcrafting, and having one profession that’s above average is better than having two. Instead of BS/JC being used by every min/max player of many classes, it’s BS with a relatively free choice for the second. The side effect though is the Jewelcrafting is slightly on the weak side for everybody.
Since primary stat gems are no longer always the best, Blacksmithing will tend to be stronger than usual professions that can only give primary stats. Jewelcrafting will be slightly weaker than standard professions. As an aside, never use the JC gems with 480 of a secondary stat.