Brand new ... there is no difference between normal teflon cables and flak jackets. But as time goes by, dust and grit will collect in the open cable system. Eventually this causes extra friction in the system that may be more than the return spring can handle (especially in Shimano derailleurs).
Ultimately, closed systems (Flak Jackets, DryCables, full housing runs) last longer. You can get Flak Jacket for $20 at Pricepoint.com. At that point, they aren't much more expensive then generics.
Finally, I would point out the error in more than one cycling book that I've seen. Some sources say you should grease your cables. In the modern days of teflon cables and housings, this is not a good thing. The grease will actually add more resistance to the system. The right stuff to use is a teflon lube.