The onyl advantage with current cards is the power configuration with the PCIe 2.0 spec supplying 75W more over the PEG slot.
However I expect most early PCIe 2.0 cards that need more juice than can be provided to offer the external power connector option like we currently have.
Long term (like 2+ years) sure it'll matter, but if you want to game now, it's not worth waiting IMO. By the time you want to upgrade again likely you'll want to upgrade the CPU and RAM.
If you're fine gaming with what you have then wait, but if you need to upgrade now (for a game like Bioshock [wait til it arrives before deciding]) then get the best you can at a reasonable price. There will be offerings from all 3 (intel, AMD, nV) for PCIe 2.0 Mobos, but whether it's worth waiting or not we won't know until the PCIe 2.0 cards tstart appearing and adoption takes hold.
Despite your statements about AGP, look how long it took for that to die off, I doubt they'd completely remove support for PCIe 1.1 anytime soon; supposedly the 1.0x stuff is an issue, but that should only present a problem for people looking at current multi-slot configurations, and IMO people who can afford Xfire or SLi can afford a new board when their forced to have it.