John,
you came up with a good point: host (or root complex in terms of PCIe) versus device end point.
When I read David's posting, I assumed he meant that the i.MX53 would be the PCI host, not the PCI device. In your (John) application you use the i.MX53 as end point.
Either way, it is hard to implement the missing hardware functionality of PCI (signals, bus and logic) using software emulation and a generic address/data bus. It would be much effort and probably outdated by the time i.MX6 is a viable technology.
I would bet on i.MX6 for sure. I'm not sure if i.MX6 supports end-point mode.