Once it comes to AGP and PCI, you can tell the difference, by a lot.
You should always stick with AGP slots, just because they outperform PCI cards dramatically. In fact, you will have a harder time running 3D applications with PCI VGA's with more memory than you would with an AGP VGA with less memory.
You will notice little difference with 64mb PCI VGA's and 32mb PCI VGA's. The PCI slot puts a bottleneck on the transfer of graphics information. AGP slots are always preferred, unless ofcourse your motherboard does not support an AGP expansion.
Stick the the nVidia AGP card instead.
If you don't believe me, test both cards on various 3D applications, then figure out the math.