I've been lucky enough to visit both JR and CI's retail locations (superstores) last week. While both were impressive in terms of sheer retail space and selection of cigars, I was far more impressed by CI.
I found JR to be a bit like a Walmart of cigars and assorted stuff. In light of their top notch catalog, I found the B&M to be a bit of a disappointment. In order to get a single, you actually have to ask a clerk to pick one from behind the counter. You cannot select you own. JR has no lounge in their Paramus location. Instead they have a store within a store that sells cheesy toys and gifts - the kind of imports you see at a highway truckstop.
CI, on the other hand, was a far more enjoyable experience with a knowledgeable / courteous staff and a much more refined and intelligent approach to retail. Singles are not only encourage, but you can mix and match with the 6th stick free and it's pick your own. CI had a very large lounge with overstuffed leather couches and two huge flat-panel widescreens . When I arrived about 3PM on Sunday, the lounge was packed with other "brothers" enjoying the fruits of their labors.
All things being equal I will be returning to CI again and again.