According to Nachmanides there were two primary reasons for the census taken by Moses in the second year in the wilderness: to ascertain the total numbers of the nation; and to become acquainted with each individual.
Rabbi Joseph Soloveitchik suggests that, prior to the sin of the golden calf, Moses functioned as an agent on behalf of the entire nation. Hence when he prays for them, he relates to them as an entire body.
After the debacle of the golden calf, Moses was required (using Rabbi Soloveitchik’s phrase) to act as a teacher/rebbe who sought to understand the life of each individual. From now on he was to pray not only for the general public, but also for each person in his or her moments of joy.
One of the greatest challenges of communal and political leadership is to be able to identify the needs and concerns of individuals. There are occasions when major decisions need to be taken that may be of benefit to the group as a whole, but will also involve suffering and pain to others. It is crucial that these individuals and communities not be overlooked. Each person has unique value.
Thus when Moses is told to count the whole nation according to their heads, he was being reminded that leadership includes being cognisant of the details in the big picture.