I've had both and like the Thule a little better. Some of it came down to looks but I think they installed better and aged better.
With our new 4R I looked at getting a Rhino rack. You could remove the factory rack and put in their tracks to mount a rack to. Nice and clean and totally adjustable and you can get it in the two or three crossbar set up. It is a little more expensive tho.
Vortex RLT600 Trackmount Black 3 Bar Roof Rack | Rhino-Rack