There is usually some major change that happens in graphic card development every year. However, the technology behind it doesn’t really become utilized for some time.
Phasing out AGP will take many years. So even if you upgrade to a motherboard without pci-e you should still be able to purchase and use newer graphics technologies. You may not have as much throughput through AGP.

If you are planning on using the new computer 2 or more years into the future you may want to consider getting one that has the capability to accept future hardware. Spending a little more now will save you more later in that case. If you plan another upgrade within 1 – 1.5 years you may hold off for the technology to become more available and cheaper.

Just because you have the slot doesn’t mean you need to get the card right off for it.

Personally I’m still waiting on the next set of breakthroughs in GFX tech probably available next year. In my opinion were in an odd year that’s a stepping stone to something much greater. As I’m looking forward to U3 ^_^

Im thinking: Is an Normal PCI card capable of running modern games?
cause if so i will buy a motherboard with PCI-E and buy a PCI-E graphics card later when they are cheaper.

I was thinking about:AOpen GeForce FX5200-V128
or something similair.

No. The fastest PCI cards I can find are based on the Radeon 92xx and Geforce 5200-5700 chipsets, and these are inadequate for high-end gaming. You need at least a 6600GT to achieve decent framerates without sacrificing too much image quality. You can "run" most current games on the slower chipsets, but it won't be a painless experience!

It also remains to be seen if manufacturers will continue to use AGP for newer chipsets. Granted, there are plenty of previous generation cards in AGP format, but it's unknown if the new chipsets will be released using the older technology.