I went with the FJ, simply because it fit my budget better. I already have a Honda Pilot, and the 4Runner just felt like overkill. I will use the Pilot for trips.
I was pleasantly surprised by the comfort and stability of the FJ. It beat my 2003 Pathfinder hands-down in comfort and road manners. The Pathfinder is a good vehicle. The FJ is a great vehicle. If you have driven a big truck and know how to use mirrors, then visibility is a very small issue. I have driven some semis, so the FJ doesn't bug me.
I have the Trail Teams edition, and I really love the suspension and features this thing came with. I feel like a kid when I am driving it, and that is good for me! I have a 4 year old that climbs into the back with no issues.