Yeah, there are a number of factors that play into off-road capability, and a stock Jeep definately has the advantage over a stock FJ for the following reasons:
1. Ground Clearance - the stock Wrangler has 1" more ground clearance than the FJ. While not a huge amount of additional clearance, I've taken rock hits on my skid plates that would have likely been much less significant with an additional inch of clearance.
2. Solid Front Axel - the Wrangler has a solid front axel stock, while the FJ is independent front suspension. The solid front axel allows for more articulation for getting over difficult obstacles. It also offers more durability, as the axels are extremely beefy. The downside to the solid front axel, and one of the reasons the FJ rides so much better on the road, is that it makes for a very harsh ride on pavement, because any imperfections in the road are picked up by both wheels at the same time since they are connected to eachother.
5. Shorter Wheel Base - If we are talking 2 door wrangler, the wheel base is about a foot shorter than the FJ's, which makes it a lot easier to get over tall obstacles without getting hung up. If we are talking the 4 door wrangler than the FJ has the advantage as it's about a foot shorter.
4. Sway Bar Disconnects - the Wrangler has sway bar disconnects which allow for more suspension travel when offroad, but they can be recconnected with the push of a button for onroad stability. The FJ's sway bars are bolted on, and it isn't practical to unbolt them for offroading, then bolt them back on when you get back to pavement.
With the above, the Jeep definately has the advantage off-road. An FJ can still keep up, but the Jeep is going to be able to do everything easier. However, I think the FJ blows the Jeep out of the water as far as onroad handling and comfort goes. That's why I went with the FJ. It's my daily driver, and 99% of the total mileage I put on my vehicle is on pavement. Now if I were in the market for a vehicle specifically off-roading, I'd buy a Jeep.