Personally, I prefer the factory top. I think it looks better and offers more cargo room in the back. They also fit very nicely and the new premium top fabric that comes with the dual top is excellent, an improvement over the older material like the Trektop uses.
2013 JKU Sahara, Gecko Green, loaded up
AEV 2.5XT lift, 315/70/17 Duratracs, AEV Pintler wheels, front/rear bumpers and hood, Warn 9.5cti-s, Teraflex carrier/hinge, Yukon 4.56 gears