So how about these two conditions as proposal for a compromise,

1. by default MSQ stays as it is, by default one needs to go through the MSQ and finish the final MSQ trial to get to end game content, if a player does not want this they have an option described in number 2.

2. There is an NPC that can be talked to that would allow the MSQ to be marked as completed for purposes of unlocking content, the player will have to go through a couple warning screens saying this option will impede their enjoyment of the story in certain quests. This option would also allow them to go through the MSQ at their own pace but like I said some of the cut scenes from endgame content might spoil the story if they aren't skipping cut scenes/

Would this be a fair compromise?