Also, you take High Capaity leaders for the Longterm potential
Early game, I might care more about the immediate benefits (shaving some turns off of research/modelling, more BP per turn etc.), before going for long term potential. So it looks like first estabilishing my regime with happy (but potentially unskilled) leaders, and only then trying to find spot replacement with high cap ones.
Also - happy leaders are immediately effective across the board (skill/tasks). Since leaders improve in the skills they use, broad based leaders (governors, supreme council director) spread their xp thinly and broadly, and take a very long time to get somewhat ok at at least a few skills. So only for very narrowly focused leaders (shq, military/modelling/applied engineering) will high cap character become proficient fast enough to compare to a bad but very happy leader - after a while.