I just bought a
2006 WK with the 5.7L HEMI and QuadraDrive II. I've only had a few months, so I can't offer a lot based experience, but here are my thoughts:
The previous generation (the WJ) had solid axles front and rear, and offered a softer ride, SIGNIFICANTLY more articulation on the trail, and slightly more headroom in the interior. The suspension on the WJ is basically the same as the Jeep TJ, and parts and aftermarket support is plentiful.
The WK is totally different. It came with multiple engines; 3.7, 4.7, 5.7, and the 3.0 diesel. From what I can tell, the 4.7 is more common, and the 5.7 is more desirable, although the diesel certainly has its fans as well. The QuadraDrive II is the way to go for sure, it basically has lockers in the front and rear diff's, as opposed to a more braking oriented traction control system newer vehicles have. Jeep sold over 500,000 WK's, so parts are widely available, though they may not be exclusively for the WK. The Commander is the exact same platform as the WK, and Jeep being Jeep, there are a number of common parts from other platforms like the Liberty and TJ that will match up too.
HOWEVER, the off road aftermarket for the WK is very small. You CAN find most everything you need, but it is very evident that this platform is out of favor. A number of mfr's have recently discontinued their products related to the WK, which is frustrating. Steel Armadillo, Rocky Road, and HK mfr'ing are good examples of what is left of the market.
Being IFS, the lift potential is limited. SuperLift used to make a robust 4" lift system, but its off the market, as is Mopar's own lift kit. With the SL, there are guys running 35" tires, but without it, you are pretty limited to 33" tires, and even then, mod's have to be made to fenders and bumpstops to make that work. OME springs and shocks will net about 3" of lift, but very little articulation in the front, which makes that QuadraDrive II system very important.
The interior of the WK is pretty nice, but its not great for tall people. I am 6'-7" and have to hold my head at a bit of an angle or sit in just such as way so that I fit under the sunroof.
The rear cargo area is not great. Poorly designed and with very little cubby space compared to the WJ that preceded it. The tie down points are not very solid, and the walls have no cargo space built in. The door pockets don't have cup holders, and there just isn't much storages space in general. I really miss the near infinite storage space of my LR3 compared to the WK. The "floor" of the rear cargo area is a removable molded plastic tray with a shallow storage area in it, but I am considering removing it altogether and building my own floor with true tie down points better suited for my typical camping load out.
The fold down seats are good and easy to use, and result in a nearly flat floor, but the total length of the cargo area is short, and I highly doubt anyone sleeps in the back of a WK. Certainly not someone my height.
The HEMI is pretty solid motor. It's the same engine in the Ram pickup and a variety of other Chrysler products, so parts are plentiful, issues are well known with fixes and solutions for everything you might encounter. The system that turns off half the cylinders under light load takes some getting used to, and the intake system needs to be closely monitored to keep it clean. An Oil Catch-Can is HIGHLY recommended to help keep the intake clean. The EGR system on the HEMI causes excess oil build up in the intake and on the throttle body, which is all electronic, and can produce a myriad of perplexing faults, that are ultimately easily fixed simply by cleaning it. Another know issue is that these V8's (4.7 and 5.7) are known to drop valves. The hydraulic lifters get gummed up after 100,000 miles or so. Pretty easy and inexpensive to fix as a preventative measure if you don't mind getting your hands dirty, or just pull off the heads and send them to a rebuild shop for $400-$500 to build the heads and you'll be golden for another 100,000 miles. On the other hand, pretty expensive to fix afterward if you tweak a piston due to a dropped valve
Lots of good info on JeepForum.com and JeepGarage, which has been super helpful during the course of my build.