I run both, depending on the weather. Unfortunately I am currently running with my hardtop as I have a puppy that refuses to stay in the cargo area. With the hardtop, I am able to fit a barrier between the rear seat and the cargo area and that keeps him out of the copilot's seat.
That dog would drive the Jeep if I let him! Once he is better trained to stay in the back, I will go back to the soft-top in the warmer weather. Until then, thank goodness for air conditioning!