I have both. I started with a 2006 Limited 4Runner V8 which my sweetie now drives. I drive the 2008 FJ TT. Here are some thoughts that might be helpful:
1. Room. The FJ is a few inches wider, and a few inches shorter. It feels more spacious to the driver. I am 6ft with wide shoulders, and for me the 4R now feels cramped. Because its a little wider, 3 people actually fit better in the back seat. However, the suicide doors are a little harder to deal with, so back seat passengers complain sometimes getting in or out. I think kids would have no problem.
2. Cargo space seems about the same with the seats down, but the FJ is actually a little less. The 4R is more convenient because the seats actually fold flat. The FJ will not give you a flat floor. As a practical matter, I have found the FJ easier to deal with for most cargo, mainly because the interior surfaces are more durable. I don't worry about scraping or tearing leather.
The cargo space behind the rear seats is definitely less. However, the roof rack works well. I also freqently use a hitch rack for family trips to carry excess luggage and making loading easier.
3. Off-road performance. The FJ runs circles around the 4R. No camparison. I can go places with the stock FJ I wouldn't even consider for the 4R. This is because of a combination of basic geometry (wider track, shorter wheelbase, better clearance) as well as the FJ Trail Teams extra features (A-Track, locker, etc).
4. Mods. There are almost no aftermarket parts for the 4R, but the FJ is a different story. Even in the last 2 years there has been an explosion of opportunities.
5. Ride and comfort. The FJ lacks the more genteel qualities of the 4R, like heated seats, full size nav system, heated mirrors, and so on. However, I have enjoyed the simplicity of the FJ. Feels more like a truck, and the ride is every bit as good. The ride off-road is amazing.
6. Performance. Once in a while you will notice you don't have quite as much power. The 4Rs V8 is great. Day by day though, I don't miss the 16mpg mileage. I routinely get 18-20mpg, even with the TT's options, and plenty of power for everything I need.
I know I haven't answered all the questions. Shoot me a PM if you have any more.