Having had chance to gather my thoughts a bit more, perhaps some of the main duties could be made into side quests, so they still have a purpose (which would satisfy myself having a "reason behind each duty", but not sure how others feel about it)? Of course, there are some that are crucial to the development of the main story arc, and those would have to remain in the mandatory MSQ unfortunately, such as:
Ifrit/Titan/Garuda - these are important plot points which build up our character as an "Eikon Slayer", and thus are a major part of our character development
The Praetorium - this is the coup de grace of A Realm Reborn, and is the climax of a major plot point built up throughout the levelling experience
Keeper of the Lake - this is a crucial plot point that is expanded upon further in Heavensward
Chrysalis - one of your main Scions is captured and you're having to free her
Steps of Faith - this is what allows you to be considered to be entrusted to enter Ishgard
The Aery - this is where you first defeat Nidhogg who is a major plot point throughout Heavensward
The Final Steps of Faith - defeating Nidhogg again after a major NPC became him
Ala Mhigo - important dungeon where you take down an important NPC throughout Stormblood
Castrum Fluminis - the primal associated here is a very import
There may be more, but these were the first examples I could think of off the top of my head. Those that are removed from the main story would still remain as side quests, for the dungeons/trials that have a lesser impact on our story development. That way, there's still a reason to go through the duties if you still wish to explore them, but would also allow for a reduction in the amount of mandatory story quests you would have to go through. I'm trying to come up with ways to please as many parties as possible, which I'm sure you can understand is a LOT easier said than done!