For us, the roof rack that fits us the best is the Thule Hullavator Pro Kayak Carrier. It is probably the most complete roof rack on the market at the moment. We rate it 5 out of 5 stars as we could not find anything to complain on. It comes from a top rated manufacturer and can be adjustable to pretty much any kayak size. Moreover, it makes loading a matter of seconds and can take heavy boats as well.
After reading the reviews here by some users who had issues with the older clamps, I contacted Thule support and they offered to send me a set of new metal hardware at no charge. The support rep. said that most of the problems with older design were probably caused by non-use of bow and stern tie downs, and strongly recommended doing this, even with the updated mounting plates. A few weeks later I received the plates, installed them, and everything seems to be solid but I think I'll still be using tie downs just to be on the safe side. Just noticed Yakima is now making racks similar to the Hull A Ports and also recommend securing the bow and stern. Guess they're playing "C-Y-A", too.
Thule simply makes the best-engineered accessories (with the possible exception of the wheels that Yakima makes for kayaks). If you use square Thule bars, your kayak will not push the saddles forward (unlike Yakima, with its round bars). Thule bike trays have improved (the old ones had junky, tricky mounting hardware), and their new kayak saddles are elegant and attach with only one screw and can be removed quickly (unlike Yak's ugly, plastic saddles that are high, noisy, and have two difficult to turn thumbscrews on the bottom). Compare them and you'll see what I mean.