I have done both in cars and I prefer the actual short shifter, not the cut stalk. Reason being is that it is harder to control the shifter when it is lower as it isn't in an optimum position for grip.

ATX MTX swap, rear drum disc swap, drilled rotors, ported intake, optim throttle body, CAI, 7.5L MAF, adj. fuel regulator, longtube headers, underdrive pulley, no EGR, low inpedence bigger injectors, 2002 Focus Swap