I would definitely opt in getting a PCI-E mobo right now. I've been trying to build my newest computer, and originally, I was indifferent to PCI-Express and just was willing to stick with AGP, and bought the Neo 2 Platinum. However, my ordeal in finding an AGP card was just ridiculously ardous and incredibly annoying. I don't know the situation in the US, but here in Canada supplies are really low because distributors are leaning towards the future that is PCI-E and therefore are not buying as much AGP, for fear of having a surplus of card lying around the warehouse. The 6600GT for example, has been impossible for me to find in AGP format. The 6800GT was also not that easy for me to find, as stores sold out and only the online store had any left. As the newest cards come out, they'll most likely be first released as PCI-E, with AGP either not having an option at all (X800 XL for example), or being created months after the initial releases.
Moreover, as others have said, the PCI-E cards tend to be cheaper in price than AGP.
As a result, if you are a gamer that's trying to build a solid rig, I think waiting two to four weeks for the new mobos to be released AND distributed is definitely a wise option. Honestly, I want to play new games on my new setup so badly, that I've been contemplating shooting myself in the foot and just settling with the Neo 2 Platinum and 6800GT. BUT... such an option would really be crippling two years down the line, when I just feel like upgrading my video card, and I realize that: a) I have less options for videocards since most would be geared towards PCI-E and b) the prices would probably be in favor the PCI-E due to greater supply.