I think one of the biggest benefits (other than a solid front axle) is that it has much less sheet metal and glass. If you have driven a Wrangler on the trail and then drive n any other vehicle you will quickly understand this.
The tires stick out further than the body and this has benefits, offroad. Also, as you noted the approach and departure angles. You also have a better break over angle with a Wrangler t. Look under a Wrangler and then look under a 4Runner. Dragging the belly of a Wrangler is no big deal but it could be detrimental to a 4Runner.
As fire as zippering window: I use bolts to hold my driver side real window in (yes it is a soft top).
On the jeep my top is ripped a little, window are glazed over but it is a Jeep.
I had a Grand Cherokee before the 4Runner and the grand was MUCH more comfortable then the 4Runner but it sucked towing compared to the 4Runner. The Grand would get about 16-18mpg the 4Runner about 20-24. Towing with the 4Runner I get about 13 and about 8 with the grand.
The 4Runner is great for what it is, so is the Wrangler.
I know quite a few people with the new Wrangler and the only issue I hear is the engine lacks power and terrible gas mileage.