Capacity, access and organization. Now to be fair I only have personal exposure to using the standard 3 pocket rugged case. I know JB offers these odd bent velcro dividers that can be used to break up the large pockets, but it's a bandaid at best.
I borrowed a Predator Urban case for my recent road trip and it's not even a fair comparison. The well organized carrying capacity of the urban is light years ahead of anything I've seen from JB. Regardless, the storage on the rugged seems more like a necessary evil then a design consideration. I understand that JB will for the most part build what you want. If you want to topple down that rabbit hole.
Right now, I think the best option on the market is the Urban with the JB interior combo. Problem there is only my moral obligation to own nothing Predator...lol
Unless I can find something that compares to JB's interior and has decent secondary storage. I will not replace my rugged. I care more about my cues then a pocket to hold loose change.