Factory vs. Yakima…
I have the Yakima control tower setup on my Outback, which replaces the stock sliding crossbars. The disadvantage is the control towers raise the height of the bars another two or three inches, making the crossbars even higher than the stock setup, and there is a little more wind noise up there. The real advantage I can see with the Yakima setup is the wide bars, which stick out past the roof line, making it easier to get a boat up there. They also seem more solid than the stock bars, but its really only the width of the bars that makes the real difference.
I replaced the stock setup on mine because I wanted to use the kayak carriers I already had which only fit round or square bars. It definitely would have been cheaper to just buy a new carrier that would fit the factory bars. I did carry a surf boat around with the stock rack and it was fine, but that thing is only 8 feet and 25lbs. I wanted a j-style cradle for my plastic Delphin, so I wouldn't have to strap it onto blocks or bars, and possibly oil can the hull. I might have been better off just buying new carriers, or trying to tie the boat on upside down to the surf pads, and see if the deck carried the weight better than the hull. I got preemptive and just replaced the whole thing, especially after all the chicken little sky is falling bull I read on the web.
People have been bad mouthing the stock setup ever since it appeared a few years ago, but it seems few have actually had first hand experience with the stock setup. Maybe Matt could do some real hands on boat transporting and let us know how it works in the real world, not just on the internet.