It’s because they’re a clone army. Among soldiers, valuable qualities include courage, adaptability, persistence and average intelligence. Loyalty, discipline and willingness to follow orders are crucial. The clones might all fit this profile but a fighting unit needs variety when facing unexpected challenges.
There are also specialist duties, from technical tasks and communications to maintenance and procurement. Clones designed for fighting would not be suited to these, nor to being commanding officers. These roles require high intelligence and leadership qualities that might be positively disruptive in a Stormtrooper.