For simplicity, a mated setup is probably best. If you have a long enough wheelbase to use a divorced setup, it can open up a lot more options as far as drivetrain setup. For example, you can put the transfer case in the exact center of the rig, so that the front a rear driveshafts are the exact same length and you get the best possible U-joint angle for both. Plus the shafts will swap and you only need to carry one, if you need a spare. Also, you can lower just the transfer case to improve angles, but since it's in the center, you can still keep a decent breakover angle. Naturally you can move the engine and transmission back in a mated setup to gain the centered case, but that can't normally be done in most non-buggy rigs because of firewall issues and interior intrusion of the engine. It's all in what you want, but the intermediate shaft between the transmission and transfer case can be phased properly, just like any other shaft, to eliminate vibration. I have 3 divorced transfer case trucks, and wouldn't trade them for anything. Again, it's personal preference, and both setups have advantages and disadvantages.