I have owned a pair of 1996 LX450's and a 2003 G500. As much as I love Toyota's I have a hard time seeing what others are seeing.
From my experience here is was I have noticed.
Engine: Advantage G500, this is not even close. It is silky smooth, powerful and get between 13-17mpg but I have seen up to 20 mpg a few times on long trips on the freeway. The V8 in the G-class is also much more reliable than the I-6 in the Toyota. The Toyota never got better than 14mpg and head gaskets were a problem on both vehicles I owned. You only have to change the oil every 10-15K miles on the G500 which I love. A sensor detects how many particulates are in the oil.
Transmission: Advantage G500, again this is not even close. The Toyota has a decent transmission but the ZF unit in the Mercedes makes it look like a piece of crap. The 4 speed unit found in the Toyota shifts rough and hunts for gears but this maybe more of a result of the engine lacking power to maintain speed on hills. The unit found in the G500 is amazing. It shifts very smooth, it never hunts for gears, and it downshifts properly to reduce wear on the brakes. It also has a manual shift mode that is very useful and easy to use. It is my favorite automatic transmission ever. I even like it more than the Allison. The unit found in the Mercedes is also a stronger and more reliable unit.
Transfecase: Tie: Both are solid and reliable units. They are very different and each has its advantage, but it is hard to say one is better than the other. It all a matter of preference. The unit found in the cruiser is a married unit but hangs low compared to the G-wagon. The unit found in the G500 is a divorced unit but it is tucked away nicely between the frame rails. The G500 has been known to have issues with the electronic actuator that engages to the transfer case but it is an easy fix. It's a 20 minutes and 3 bolt job to replace the actuator. It's not like it's a PHH.
Suspension: Advantage Toyota. As stated by others the G500 does not have as much flex as other solid axle vehicles but I think this is grossly over exaggerated. I spent all of last week riding trails in Moab last week in a Stock G500 and I did not have any issues. I only lifted a tire 3 times all week and I am certain my LX450 would have been doing the 3 tire salute on the same obstacles. I did Fins and Things, Hells Revenge including tip over challenge, Tower Arch and Poison Spider Mesa. I had a great time but never once did I wish I had more flex. The lack of flex is actually nice because the chassis never creaks or squeaks. Flex is overrated and how important is it when you have lockers? Personally it is no where near as approach and departure angles.
Axles: Advantage G500; Both have lockers and are great axles but this all come down to maintenance. While the design is very similar, Mercedes did a much better job executing it. The front axle in the Mercedes will go 4-5 times longer between rebuilds.
Frame: Advantage G500: The frame on the G500 looks like it belongs under a 1 ton truck.
Four wheel Drive system: Advantage G500, The advantage goes to the G500 for several reasons. In stock form the center and rear lockers can be engaged in 4wd HI. Toyota requires a mod for this. You can also turn off the traction control/esp on the Mercedes. Traction control is nice to have, but it is also nice to be able to turn it off.
Approach and Departure: Advantage G500, even in stock form it has great approach and departure angles. My 1996 LX450 with 3" OME lift still found a way to drag it's but on every rock.
Aftermarket support: Advantage FJ80, For the most part you can get anything you want for both vehicles but you will have more choices with the Land Cruiser.
Cargo capacity: Tie, They feel about the same to me.
Driver and passenger comfort: Advantage G500, Yet again this one is not even close. I am 6"8" 330lbs and the G500 has plenty of room to spare. My wife is 6' 1" and she found the Landcruiser to be a little cramped. I can sit comfortably in the second row even though I am a big guy. I can wear my cowboy hat in the car, I love it. I love that it has front and rear heated leather. I love that it has cup holders. I have installed the rear horizontal seats and now it seat 9 passengers very nicely. The rear seats will easily hold 4 six footers and kids love them.
Steering: Advantage Toyota, the steering on the G500 feels heavy but you get used to it.
Dealer Support: Mercedes, I know this may sound crazy but Mercedes has much better global coverage. Toyota has better support here in the states. I had my Mercedes in the dealer to get the AC recharged and an oil change and they gave me a free rental car for 5 days. It took 5 days because it was over a holiday weekend. I had to pay $14 for gas but I drove that 2013 C-class over 600 miles. I also love the fact they hand wash my car every time I even get an oil change.
Forum Support: Advantage Toyota, This one is not even close. IH8hud is great support site for enthusiasts. I have noticed that the G500 owners are much more civilized and respectful but there are some great Toyota guys out there. Major props to all who are in it to help others.
Other things to consider, they are both very reasonable to insure. My 2003 Mercedes costs the same to insure as my 2000 Montero. The Mercedes take premium fuel but I have run regular at the recommendation of other G500 enthusiasts and it seems to run great on regular fuel. I am not sure it matters if you run premium in the G500. On the G55 it probably matters because it has a supercharger. The repairs on the Mercedes are pricey, but most repair can be done at home with a little know how.
I know I probably missed something, but I did my best. From my observations the G500 is better than the FZJ80/LX450 in almost every way. The shear power makes it a better daily driver. Those who say the Toy is better have never owned a G-class. Both are great vehicles but the build quality is so obvious it like comparing a Chevy S10 to a Toyota Tacoma. Last fall I had my old man drive it on some trails in Moab and he could not believe how much more solid and competent the G500 was when compared to my Locked and lifted 1996 LX450. His main observation was the G500 felt much more nimble, it had more power but never slipped a wheel and never even creaked while off road. The LX450 still got the job done but it was nowhere near as graceful. It was always spinning tires and looking for traction. A buddy of mine (MOT) from Mud struggled to get his diesel powered FJ80 into the same locations my G500 went in stock for with out slipping a wheel or rubbing once. He seemed to find a lot of rock with the rear of his rig. As far as the electrical issues with window regulators it seems to be a common problem, but they can be replaced by a competent do it yourselfer. The center drive shaft seems to be a maintenance thing. If proper maintenance is taken it seems to last a long time. How ever you dice it it is alot cheaper than rebuilding the front axle on an land cruiser every 80K miles.
While I compared the G500 and LX450 above, here are some reviews of both the FZJ100 and the G500. These guys are fantastic with reviews and they love their cruisers but they openly admit the Mercedes is a better off-roader.
http://www.youtube.com/watch?v=e1NdM1snEbE
http://www.youtube.com/watch?v=OqmK81ZBLvI
http://www.youtube.com/watch?v=R3fp8mDh5JU&feature=endscreen&NR=1