EV700 :
I feel that PCI Express 2.0 will bring about all the issues faced in the 4x/8x AGP battle.
Why?
It's backward compatible in both directions.
The only 8X / 4x issues were early poor MoBo support, which lead to the stickers proclaiming R9700/FX5800 compatible MoBos like the sticker on my old Gigabyte board. And the big MoBo makers like Gigabyte fixed the problem when it arose. So be sure to get a quality board if you're concerned.
At/near launch R600 was shown running on a PCIe 2.0 PEG slotted MoBo running with only 1 6pin power connector plugged in, and it also works in older MoBos obviously. Proving some cross-platform inter-operability.
It's really a question of providing power if you design a PCIe2.0 part and you want it to be backwards compatible it better be ready to run without the extra power and thus grab it from another source/connector, since the slots are physically the same only supplying an increase in frequency (not more pins).
Most cards will be backwards compatible leading into the middle of next generation simply because of the fact that there's not enough of an install base. After that you just have to worry when you NEED to change, not about future possibilities/probabilities.