With cable management, the key is to have a mobo that you can stuff cables behind. Either on the backside of the motherboard tray, or between the motherboad and the tray.
For example, with your rear case fan, don't run those red/yellow cables down and right across the middle of your case. Instead run it along the back edge and then flat across your power supply. Tape it down where it's less obvious and it will clean up the mess.
Bundle as many of the wires as you can, perhaps even use some vinyl tape and tape them together every few inches to keep them clean and neat. I often use velcro tie wraps. It's a long spool of velcro that I can cut to length and it just goes around the cable and sticks to itself.
It usually takes me just as long to wire my case as it does to assemble it, in fact it probably takes longer.