The point is, if you have software that is purpose written to interface with a specific PCI card, you can change the card to an equivalent PCI-E card and the software will continue to function.
The average user will probably never be in a situation where this is an advantage but for enterprises this could potentially save them a lot of money. It will make it a lot more compelling to switch to PCI-E architecture if companies only have to change their hardware and not rewrite their software.