I've had my 2012 Focus SE for a few weeks now and was aware of possible transmission issues prior to purchasing the vehicle. The car has the Sport package and Select Shift option. Overall I'm impressed with the new Focus having moved from a 2009 Focus.
The 2012 Focus is not your parents' Focus and has definitely been improved in the area of road handling and stability. The car just feels solid while tooling down the road.
Now, regarding the jerky transmission shifting, this typically occurs on the lower gears, and most noticeably when you get going from a dead stop. There is definitely a hesitation if you try accelerating quickly from a dead stop. It reminds me of the turbo hesitation in my 2008 Super Duty.
I suspect that Ford will eventually send out notices to all 2012 Focus owners for a re-flash to correct the shifting issues. I realize that the transmission is different than what is in previous years' Focuses, but if the tranny is working as designed in my Focus, then Ford needs to put a different transmission in the car.