I have the Yakima and my friend has a Thule. They are pretty similar. The rest of my stuff is Yakima so the locks all match so I went with the Yakima.
However, if you are buying new cross bars, I would suggest you get the factory bars or the Thule bars. The boxes and other accessories fit on any cross bar but the OEM or Thule bars are easier to attach. I had Yakima bars from a prior car so I used them. Once attached they are great but since the are designed to work with different cars (changing clips), they are a little more difficult to attach.
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