I found two USB 3 Transceivers to interface with FPGA. I am wondering which one is better then the other or if there exist even better choice for USB 3 Transceivers to interface with FPGA ?
If you ask about "better" you have to say in which regard.
Almost every thing is better in one way but worse at another way.
In your case it may be: price, software effort, hardware effort, noise, current consumption, part count, PCB space, temperature range, availability ... and much more.
I am considering reliability and it's usage in radiation environment. I guess software/hardware would be almost the same when it comes to USB 3 protocol.