I put Thule mounts and crossbars on my '11 CX9. The Thule mounts and crossbars are rated for more weight than factory rails/bars. I carry kayaks on the car and had a bad experience on a previous car (toyota) where the factory racks failed. Not fun.
I also bought a Yakima Skybox lowpro 15 to carry my skis in the winter. It was pricey, but was the only cartop carrier that was "skinny" enough to allow for me to drive my CX9 into the garage with the carrier on top. Just barely fits on the fixed-position crossbars. Does not hit the rear lift when it opens either.
If you get the Thule system, you will want to get the wind faring as well. Lots of whistling/noise otherwise.