Yakima for heavy loadsWell, I've used both kinds. Presently, I've got a Thule because my Saab has special Thule specific mounting points.
If you think you might ever want to use the rack to carry something relatively heavy, go with Yakima. Over the years I've seen quite a few bent cross bars on Thule racks, but I've never seen a bent Yakima crossbar. Many years ago I loaded up a Yakima rack to the point that the towers started to deform the car roof, but the crossbars did not bend even slightly.
Another thing I liked about the Yakima ski rack was the way it folded down out of the wind so easily when not in use. When folded down the racks produced significantly less wind noise.