I was out driving my Fiesta yesterday for about 45 minutes on the highway, and thought to myself that the armrest in the center is never going to work. The cup holders are under my elbow, which is where the arm rest would need to be placed in order to actually use it for an arm rest. Sometimes I drive my brothers Focus ZTS when he drives the Fiesta for a day. His car has an arm rest and is a 5-speed. I am always catching my arm hitting the arm rest, and it is folded up! We even installed a short throw shifter, otherwise your arm would get stuck between the rest and the shifter.
I do have a manual transmission car with an arm rest in the center, and that is my Mustang. However, the arm rest is so far back on the console, it could never be used for an arm rest. The car also has no cup holders.