Bestop makes the OEM tops for Jeep, so there's not much difference unless you go for something like the Trek Top NX (slant back). The Super Top is pretty much the same as the factory top.
I ended up getting a used OEM '12 top and love it. It handles so much nicer without the hard top. Plus the factory top (and super top) are nice because you can put them down easily and don't have to take anything off. So if it starts raining, you have it with you vs. the hard top you have to leave at home or camp.
One thing to keep an eye on: the '13 and '14 tops have the option of the new material (forget the official name for it, black twill?) which is thicker, looks nicer, less noisy, etc. So if you're getting one new, definitely opt for the new material.
Check your classified for a used top, you'll save a lot of money. Most will be the older material though.