My two cents, YMMV and all that...
I had a Gobi rack on my JK and while it was capable, it did add a certain amount of noise and a noticeable 1-1.5 MPG drop even when empty as I take the RTT off when we aren't using it. Also, under heavy loads even when adjusted properly it can move around a little while traversing harsh roads. While I've only experienced the Gobi style of rack, I believe that any rack with A-Pillar supports is going to experience the same issues. While the Frontrunner rack is obviously very sturdy the full length version ruins the lines of the Jeep in my opinion. I also wasn't a fan of the 16 x 22mm holes that need to be drilled into the roof!
I still wanted the option of mounting our RTT on the JK when it's not on the trailer so I decided to go with the RhinoRack Backbone system and the 3/4 length Pioneer rack. The hole drilling in the hardtop is minimal in comparison to the Frontrunner, and the entire hardtop can be removed with the rack in place. I hear no additional wind noise at highway speeds with the rack empty. I'm really impressed with the overall sturdiness of the rack and unlike the Gobi rack, accessories are available for immediate purchase.
Here's a quick pic from after the install:
We'll see how it holds up long term, but so far I'm very happy with how it turned out and the options it allows.