I think it depends how much you plan to modify it.
I think that if you are talking about a mostly stock platform, then Eddie is right- the jk is great, and comes from the factory better than any other jeep before it.
However- I don't think that is true about heavily modified rigs. At some point, all rigs are about equal. When it has the same axles, same tires, roughly the same wheel base with the two doors, (lots of people stretch tjs too), and roughly the same weight- it's capability is probably about the same and just falls to the guy behind the wheel. They just look slightly different, and cost different amounts.
If you plan to completely build it, then I don't think there is much of a difference other than looks and of coarse, the heavily sought after 4 doors, but if you only plan to mildly modify it, and are looking for factory performance, then the jk Is the way to go.