I can honestly say that B6 just isn't geared for a business traveler when compared to the legacies. Not to mention their recent "software updates" that have been affecting points posting and people having issues at check-in. As you said, they are focusing much more on the 5-10 segment a year traveler and big single trip flyers.
I don't fly that route but I do fly (as my name implies) JFK -> MSY -> JFK on B6 and occasionally on D/UA. My experience is likely skewed because of Mosaic but I've never had an issue jumping on standby within 30 minutes of a flight. I've admittedly never cut as close as you did in this instance.