CAN

Pros

• simple, only 2 wire
• no controller needed on the backplane
• range
• transceivers cheap/plentiful

Cons

• speed
• difficulty of debugging
• each board needs a CAN transceiver IC

Ethernet

Pros

• debugging is easier
  
  • talk to all boards with a standard PC
  • makes testing easier, simulation easier to implement
• works with pre-made tools
  • wireshark for debugging / capture of the network for playback
  • don't need to implement some kind of discovery protocol, just use ping
  • need some other functionality? it probably already exists
    • TFTP
    • SNTP
    • PTP
• ground hardware become trivial
  • forward network packets identically
• speed
• Ethernet device ICs cheap (Wiznet W5500)

Cons

• more complicated protocol
• would need an Ethernet switch IC on the backplane
  • this requires routing from each board connector as well as power for the switch
• each board needs an Ethernet IC