I own both a 2006 Commander Hemi / Limited w QDII and a 2008 Wrangler JKU.
We use the commander mainly for long road trips, and heading to Colorado in the winter. The extra space inside is nice, and we do use the third row pretty frequently. This thing is awesome in snow / ice and the few times I've been offroad in it otherwise it always shined. It also does great towing the EVO1 trailer and zooming up hills in the mountains without any issues. However, it isn't lifted (yet) so I know its limitations. I do plan on adding a lift to it in the next few years and probably some 33" tires just for a better stance and use if I take it to Colorado in the summertime.
There were initially more options available for the Commander, but with the limited market it seems like alot of the vendors stopped making kit for it (bumpers, gas tanks, etc.) Although recently (as seen above with the black Commander) some higher range lifts are available now, but they are very pricey, although very tempting as I love the look of that Commander. Maybe some day!
The JKU on the other hand is a dog, it won't get up and go unless I'm going straight downhill with a tailwind. But it will go anywhere, and that's why I spent the money on it first for the lift, tires, winches, etc. It is my daily driver and I smile every time I climb up in it.