Your obviously just a casual DIY computer builder...not an enthusiast. An enthusiast would take PCI-E 1.0 or 2.0 any time over a AGP motherboard. Hardware manufacturers dont build components to go backwards, they look at creating new hardware that is relevant to todays and future components such as graphic cards. AGP is no longer mainstream, it is obsolete. The reason they create 'newish' components to fit 'older' hardware is a little thing called money. They realise that not everyone is an enthusiast and as a result milk the old cow so to speak.
You talk about graphic card manufacturers creating the equivelant of a gtx 260/280 on AGP....well ok even if they do it wont be before there are newer maybe PCI-E 3.0 graphic cards that are double the power of the GTX 260/280. Sorry dude but you are so LAST GEN.
You hit the nail on the head when you said old school. A PS2 is backwards compatible to PS1 game but a PS3 isnt (correct me if im wrong)....does that make the PS2 better than the PS3? absolutley not.