2.4 Puma with over 170.000 kms and there is no clunking on changing gears. The clutch has been changed owing to spring rattles. Still on the original adapter shaft. I find the Puma engine/gearbox set up extremely smooth and relaxing. I also have a 2011 Puma and that is the same. First gear is very low in the Puma and some people surge it when taking off from traffic lights. I also have a 110 200 tdi that I have owned from 1996 and this is also smooth to drive but the clutch is heavier than the Puma clutch. There is no clunking on changing gear in this either. The change from high to low on the Puma is very smooth and easy to use, much more user friendly than the tdi.
Worn bushings could be a factor in the equation.

