I personally wouldn't go to the trouble of all-new wiring unless the new equip is so high power that the existing wires couldn't handle it.
I have used a wiring harness for the head unit that makes it a snap to put in any stereo or take it out and replace with the factory. As far as speakers go, if you're just replacing the speakers themselves, why not connect them to the original wires? You could probable unplug them later and plug in the old speakers if you sell. Also, I hate running wires through the flex conns from the body to the doors!
Just my 2 cents, eh?
