I think part of the problem in Brooklyn is that there isn't a lot of space for the in-transits to wait in the terminal, and itisn't very comfortable. Nobody is allowed back on until everybody has cleared immigration. So if one last person dawdles, the rest are left 'captive.'
I've heard Vancouver can be bad, but the one time we were in transit there, we spent the day off the ship, sightseeing, and by the time we returned all the in transits and most of the newly embarking passengers had been processed. If I find myself in the in transit situation again, I'll take a tour or go out sightseeing.
Except for the time an idiot took one of my suitcases, I have found luggage collection to be easy in Brookyn. The crazy thing was, the staff that are cranky handling embarkation (especially the gorgon who guards the entrance to the grills/platinum/diamond waiting area) were exceptionally kind and helpful, tracking down where my case went.