Neptulon was already free in Legion, and part of the Shaman Order Hall stuff. They just cut the explanation. Originally there was a Vash’ir raid planned that would have resolved that story, but that got cut, or so I heard.
To quote WoWpedia:
The likely reason Blizzard had Neptulon end up freeing himself off-screen between Cataclysm and Legion is because the Abyssal Maw raid, the planned conclusion for the Vashj’ir storyline, was canceled. The situation was described by Chris Metzen as a “damn mess is what it was.”
https://wow.gamepedia.com/Neptulon#Notes_and_trivia