I posted this on the Battle.net forums, but knowing the responses I'm likely to get down there, I decided to start a discussion of the same topic here.
After spending all of DS as the undisputed inferior profession in terms of stat bonuses, JC is once again the runt of the pack going into MoP.
Because secondary stat budgets are now doubled on gems, this changes the way we slot our sockets. If we have a secondary stat that is weighted more than half of our primary stat, we are now supposed to gem pure secondary stats in blue/yellows, and hybrids in reds.
The JC exclusive gems were not given double budget for secondary stats, so we're still stuck with pure reds for JC gems.
However, this 320 extra stats from JC gems requires a red gem in a red socket. This would have been fine if we were gemming pure reds in red sockets anyways, but now we have a better option in the form of hybrid gems with double secondary stats. To obtain the JC stat bonus, we forgo the superior hydrid gem in favor of pure reds.
Because of this, the relative gain of using JC gems is LESS than 320 stats.
To fix this, the best option would be to provide hydrid JC gems that provide extra primary stats, such as +240 (80+160) strength and + 160 haste. This allows us to gem hybrid serpent's eyes while still obtaining the same +320 stat bonus standard on professions.
EDIT: Since apparently gathering professions are somehow still being taken into account when determining BiS professions, I will now say this explicitly: I am ignoring the gathering professions because their PvE bonuses are and have always been completely negligible.
Also, I'd like to point out that this argument only applies if you play a spec with a secondary stat weighted at more than half of your primary stat, but less than your primary stat.