So, a lot of truths spoken here. I have an all Thule setup. My 4runner only came with the mount points for the tracks, but didn't actually come with the factory tracks. You know, those black pieces of plastic that run down the length of your vehicle?
Thule (and Yakima I'm sure) tracks are super easy to install. You just need a drill to drill holes that align with the roof holes, a saw to cut the length down a bit, and some patience. I went with Thule because I work for a Thule dealer and there was an employee special on them.
Anyway, I have the MOAB basket and I leave that connected to the foot pack that connects to the rails. Basically, I find it easier to just remove the crossbars and the basket (four locks) versus removing the basket (four locks and eight wing nuts).
I don't have it on unless I need it...and honestly that's rare. I bring it camping, climbing, etc. and it's great. I happen to think it looks better than the Yakima Load Warrior, but that's just my opinion.
Good luck with whatever you decide! I know REI is sending out a 20% off coupon for members for the upcoming Anniversary Sale. It's a good way to get a better price on that stuff.