The YJ I just bought came with a Bestop "Sunrider" which is Bestop's version of the flip-top. I like the way it mounts to the windsheild, but I doubt I'll ever use the flip-top feature. It seems like a good idea, but I don't care for it. It's just not something I think most people would use much, I mean how long does it really take to put down or up a soft top once you get the hang of it? not long.
One big benefit to the pavement ends top is the price, but I believe the windows and material are thicker on the bestop tops. Call a 4WD hardware or quadratech and they'll give the specs.