> the MPC8641 has more PCIe lanes (although only 1.0)
Yes, it can dedicate up to 16 SerDes lanes (x8 x8) to PCIe. But as you say, that only equals 8 lanes (x4 x4) when compared to the QorIQ P5's PCIe 2.0. So overall, the QorIQ P5 can dedicate up to 50% more bandwidth to PCIe than MPC8641(D), or up to 25% more bandwidth in a configuration suited for desktop computing (i.e. with on-chip SATA controllers enabled).
> and PCI slot capability.
Neither MPC8641(D) nor MPC8640(D) incorporate a PCI controller. Do you mean the MPC8610 here maybe?
> The e600 is dead.
...as soon as the AltiVec enabled QorIQ T is there, yes. Regardless, Freescale will offer the existing MPC86xx chips for quite some years to come.