Ideally, I'd like to see it as a list of what items we want to show or hide on the map (or mini-map), whether that's MSQ, side-quests, levemetes, shops, Triple Triad NPCs, etc. But yes, having the Main Scenario a separate option on that list from other quests would be nice. I could actually see quests alone being divided into about six categories:
• Main Scenario Quests
• Class/Job quests
• Daily repeatable quests
• Sidequests that unlock features or dungeons
• Seasonal or promotional event quests
• Other sidequests
(All perhaps under a heading for "Quests" that lets people check/uncheck all of them at once when they want)