[replicant_argent]

I ran Thules on both my Explorers for years, never had a single problem with them. Solid and pretty bombproof. Quite frankly, I think both systems will do you well, and have a proven track record. I liked the thule square bars because they seemed to hold a load solidly when hauling 2x4s or materiel up top, (the flat rubberized coating on the bars with a bigger surface area than the round Yaks. Could just be a false impression, though.)
If one of the companies accessories looks better or more useful for you in your philosophy of use for the things you will be putting on it, and the price differential makes no difference, go with the most "YOU-friendly" system.