i have not heard about the wattage cap on PCIE slots. Regardless if a GPU supports PCIE 2.x and you put it in a PCIE x16 *(Gen1)* slot, you will lose "optimization" i guess you could call it.
if you had identical GPU's just say two Nvidia 9600gt cards and one was x16 and one was x16 2.0 the one with the PCIE 2.0 would perform slightly better just because of optimization. It would not perform better because of bandwidth limitations or power limitations.
here is a quote from another forum that i dug up from toms hardware"
BEGINNING OF QUOTE
"Picture driving a Prius on an 8 lane highway with a 200mph speed limit and no other traffic. Now increase the speed limit to 400mph. That's about how useful PCIe 2.0 is to any 8800 class GPU (or any modern day GPU for that matter).
Oh and in case you were wondering, PCIe 2.0 is fully backwards compatible with PCIe 1.X."
END OF QUOTE
its an older post but it gets the point across. The slots are backwards compatible. but imho it depends on your budget as to which is the better investment because you would be losing less performance with the GTX 460 over the 470 but the loss difference would be minimal. the GTX 460,465,and 470 are all about the same in the price to performance aspect. don't get a gtx 480 unless you have nothing else to spend your money on.
i wouldn't base a purchase on a GPU over the x16 vs x2.0 slot. but that's just me
hope this helps.