Offered the choice between two similar priced products, I do believe a Thunderbolt (PCIe) NIC would still be the better choice over a USB one. Especially when the USB choice is USB2.
I'd agree, though the notion of "similarly priced" can be a slippery one. In the UK, the Apple Thunderbolt NIC costs
£25. The Apple USB NIC also costs
£25. But USB NICs that do not have Macintosh drivers cost
a tenth of that.
This is one reason why Apple have a larger market capitalisation than Boeing. If you buy a first-class seat on a Boeing, you get to swank around in a nice lounge where people make you cups of coffee. If you buy a first-class seat in front of a Macbook Air, they still Easyjet you on the accessories.
Peter