Just my feelings, but for a road bike I feel the fork mount is more sturdy and solid. Plus the bike doesn't look like it sits ridiculously high.
For a mountain bike I would think the mounts allowing both wheels to stay on would be beneficial. I don't like taking off and putting on my mountain bike wheels for car transportation, and am always afraid of accidently squeezing the brake pads without the disc and wheel in place. I still use the fork mount though.
I have a Yakima system. The fork mount system I have is either the 2nd or 3rd best one...not the best one that is prettier looking. I forget the name; either viper or copperhead or something.