pci slots will be around for ages, pci-e is just a superset of pci. agp is nothing but a 4x pci slot. so it shouldne bt much more hassle but agp slots limit you to ... agp cards only.. pci slots let you put in anything pci.
pci isnt going anywhere (in a world that still ships psi and rs232 connectors on mobos).
at least with pci-e its more than just gfx cards (unlike agp).