First off I'll state that I don't know enough about Jeeps to hurt myself...
GF picked up a 2 door, JK Rubi a while back.  I think it has stock suspension, 35s and flares to clear and cover them.  We took it out first seriously for a week of good trails in the Okanagan area  last month along with my truck and a few others.  The JK did great, but we both agreed that the ride in a fair bit too rough...
We got back and I figured ten seconds on the internet would reveal lots of discussion, but I'm seeing nothing.  Must be that everyone puts up with it, I don't know.  If my reading on spring rates is correct, it does not sound like that is the problem.  Is it just stiff shocks?