you won't notice the difference between pcie 3.0 and 2.0 since the graphic cards of this generation don't use that much bandwidth.
if you have 8Gb of ram and the new gpu you should be able to play BF3 just fine.
Do you have a core 2 duo or a core 2 quad?
To run Bf3 you need a core 2 quad which runs at roughly 3.0ghz to get it to run smooth, its a very cpu intensive game.