The efficiency in charge and discharge of a capacitor should be very high as long as it doesnt have to store the charge for too long (when internal resistances will cause it to slowly discharge itself).

The factor of 1/2 is down to the pure physics of it - its nothing to do with efficiency. (in fact, the equation is the result of an integration of C x V with respect to voltage, in the same manner as integrating momentum (m x v) with respect to velocity results in kinetic energy - 1/2mv^2).

I assume you are using supercaps since you are talking capacitance in Farads. Just remember that these generally have a maximum voltage of 5.5V. They WILL blow up if you exceed this! You could try putting them in series to get around this, but this would reduce the overall capacitance (2 1F caps in series = 0.5Farad).

What are you trying to do exactly?