Having done dozens of cruises from Manhattan on at least 6 different cruise lines, yes some were not problematic but some were total nightmares at embarkation, disembarkation, or both. To put it bluntly, your lone cruise is meaningless as a measure of the experience of cruising from the port. On another day your experience could have been completely different.
NCL runs relatively few one way trips beginning or ending in NY. I recall one or two in the past being scheduled to depart Brooklyn, but the overwhelming percentage of NCL cruise passengers are on roundtrip voyages. Moving a few cruises doesn't address the core issues that affect probably 95% of NCL's NY passengers.
Did you forget what I documented for you about NCL having to deal with the same service providers regardless of whether they sail from Manhattan, Brooklyn or Cape Liberty? Moving a few cruises is going to do nothing to address the problems caused by having to deal with that Hydra...and I need to add the Coast Guard and USCBP, which can delay any embarkation and disembarkation.