PCIe channel is way more demanding for design implementation, and it's also point-to-point interface.
Meaning that your CPU is acting like a host, to which you connect target devices. I'm not familiar with i.MX series, but be sure to check if you can connect two ARM's together via their PCIe link, as that may require adding a bridge between.
So Ethernet is for sure more versatile solution, and you can also use it to interface slower devices (which cannot cope with PCIe interface directly).