It seems that other than commute times and traffic, the only other thing you might be missing out is that you have zoned too many commercial zones. Keep in mind that all zones prefer to develop laterally rather than vertically. Try removing about 20-50% of your CS$$$ and CO$$$ in strategic places and those commercial businesses will start crowding in the rest of your commercial zones. Also, don't foget that only CS$$$ and CO$$$ have skyscrapers. Hope this helps.