PCIe != AGP. Basically, it's very hard to ramp up the speed any further on AGP, since it's an *extremely* wide bus (150+ wires, I think, compared with ~30-40 for PCIe x16). The signalling gets very, very hard to do reliably at those speeds -- they've already had to reduce the signaling voltage spec *twice* (from 3.3V to 1.5V to 0.8V for 1x/2x, 4x, and 8x AGP, respectively). It's reached a point where it's not worth trying to make it any faster.
PCIe was built with much higher bandwidth in mind, and because it's set up as a bunch of serial links, it's easier to scale. That's about the simplest explanation I can give.
Also, as noted by Dave, AGP bandwidth is not the limitation holding back video cards these days.