It is down to personal preference.
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However most experienced machine builders, will recommend Ethernet over USB. Over 99% of USB users never have any problems, even when questionable wiring techniques have been used, yet others, even with proper wiring techniques will have endless problems.
The fact is though, the only threads over on the Mach forum about intermittent communication issues are all about USB controllers. I personally cannot remember seeing any involving Ethernet, apart from initial setup problems.
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PCs can have more than one Ethernet port installed, it's just not a common thing to need. There are people who run Ethernet devices over a full network, but ideally you should be dedicating a computer to running a machine and connecting directly, with the same advice applying to USB.