I'd imagine this is part of the reason they are implementing the new game plus feature. In the past week I've had over half my previous WoW raiding guild that i was in join the game, I gifted the ARR story skip to a friend because we all want to raid together in ShB and they honestly didn't want to deal with the 100+ MSQ quests post-50 and because she wanted to catch up with her husband that's working on Heavensward content. She can always go back and replay parts of the MSQ story that she skipped with the new game plus feature in Shb.

I don't think they are ever going to remove the MSQ requirement to progress in the game, nor should they. There's people out there who honestly just want the raiding aspect of the MMO and don't care about the story and that's what the skip books are for. I think with new game plus implemented everything will even out with giving the players the option of how they want to play the game and more options is always a healthy solution when it comes to a MMO.