I assume you mean the difference between using Yakima crossbars with Lowriders (The Mighty Mounts are meant for factory crossbars):
Versus factory crossbars with Mighty Mounts.Image courtesy Yakima and RackAttack
Yakima crossbars with Lowriders win hands down. They are easy to install (5min or less), far more versatile (they accept a wider range of Yakima accessories), can be had in different widths, and best of all they're universal so they can be easily transferred to other vehicles. I use 58" crossbars and it works well on the Rogue as it provides some vehicle protection and easier loading. I also use Yakima Gunwale Brackets which only fit round or square crossbars to carry canoes, lumber, ladder, etc. and I also have an older Yakima ski rack attachment. The only downside to Yakima's crossbars is they are noisy at highway speeds when unloaded. You can remedy this by getting a wind fairing. I have used the rack extensively and fuel economy loss is minor if any... and I regularly carry an 8ft stepladder! I do remove them when not needed for a clean look and less noise though.
Factory Crossbars with Mighty Mounts are somewhat limited. They are meant for Yakima's ski/snowboard and bike racks. They aren't much good for carrying big stuff like lumber or a canoe. I've used Mighty Mounts on a previous vehicle and they are a bit more work to mount/dismount than Lowriders as it involves removing the ski or bike attachment first. Also, the convex curve of the factory crossrails and the fact they are just painted make it difficult to load flat items and secure them properly. I guess the upside is the factory crossbars are very aerodynamic and shoudn't cause any fuel economy loss.
You can see more pics of my setup here:
zerothread/318590