Out of curiosity, why are you going to communicate to the FPGA over Ethernet vs PCIe or SPI or USB? It seems like you'd have to do a lot of high level processing on the FPGA to get it behave nicely on an Ethernet network.
With UDP and custom FPGA IP for handling the packets the processing works fine. Network behavior is made easier as the IO board will mostly be used in a dedicated point-to-point Ethernet connection.
Our opinion is that Ethernet is easier to analyze using tools such as Wireshark, in addition to being easier to run in a cable between different PCAs. It also allows the IO board to be easily networked for communicating with development tools to reprogram the FPGA memory, debug issues, do testing from a developer machine etc without concern for driver issues on various host operating systems.