I'm not sure what you're angling at here, but... no. From a programming standpoint PCIe can be treated like an evolution of PCI but the physical implementation is completely different. PCI is a conventional parallel bus with multiplexed address/data lines while PCIe is a point-to-point serial topology with transfers encapsulated into packets. Electrically they're not alike *at all*. Converting from one to the other requires a bridge chip, it's not just shuffling wires around.
Note that said bridge chips *most of the time* don't cause software problems but your mileage may vary depending on the card, particularly if it makes extensive use of DMA/bus-mastering.