Yes, in saints row 2 he was more "i will do anything i have to do to complete my missions", he was more objective and serious not a idiotNo. The "new" boss is a cartoonish pussy, and a shadow of its former insane glory.
Sure Johnny is scary, but he lacks of the ability to rule a gang. The Boss has this ability because he is far more 'creative' than Johnny and very able to organize plains. Also he is very loyal and trustworthy, and his friends know that he will never betray them. They don't respect him as authority, because they see him more like a friend, or a brother. Before I though the Boss was lonely. He has been lonely, but slowly now he seems more appreciate, not as leader but as person.