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I may be a conspiracy theorist or something, but I really think the only reason that graphics cards really shifted to pci-e in the first place over agp was so they could do dual card solutions and hopefully sell more cards to people.
I've read that a x16 pci-e slot has double the bandwith of an agp 8x. So 8x pci-e which will run cards with no issues and did the dual card thing for some time has enough bandwith so an agp slot had enough bandwith.
So the only reason I have left as bandwith wasn't the issue is that they wanted to do dual card stuff to sell more cards. I don't see pci-e really being a huge thing in the desktop segment as people don't need the bandwith of pci-e 1.0. Though I imagine it'll be foisted upon us if we like it or not by chipset manufacturers much like pci-e 1.0 was.
EDIT:: To better answer the question. Since it's a very scalable interface in terms of performance and adding more slots and such I can't see it going away. If AGP could have been as easially used for other things or had another slot added for dual card solutions and all we may still be using it today. As said it will be upgraded, but I doubt it'll change enough to make the old stuff not work with the new. It's possible as they may be changing clock speeds or something, but I think they'll make sure the new slots work with the old cards due to the fact that there is a lot of pci-e 1.0 stuff out there being used and consumers don't like big changes that make their old hardware not work anymore.