Ok, but that still requires quite a heck of a rework regardless. How is the script going to be affected since now the player isn't invested anymore? Do certain details need to be altered to accommodate the new changes? Will voice acting need to be redone? If an NPC can just do the quest for you, then why are you even there in the first place if you have no purpose?
Regardless of how much you hate fetch quests and boring story, everything leads to a build up in relationship with other characters as the story progresses. This is nothing new and it's not even exclusive to MMORPGs. Pretty much every RPG has you doing stuff NPCs "could" do themselves, but they ask you and at least thank you for helping out, thus, depending on the story, they can trust you later or at least have some story and character development. World building is the term I think, but if everyone could just do everything themselves, then there'd be far less game to play and you'd wonder why all you do is just kill everything and nothing else.
People seem to be stuck on this belief that (general) we don't want people skipping the story because "lore". I'm saying it's not an option because of the crummy system the devs have in place; they can't let people only skip certain quests without it affecting quests ahead of it. Heard of sequence breaking? That's what the whole thing entails to. Do things in a different order or skip certain flags and the game will freak out and break certain things, which means even more time wasted patching a system for a bunch of players that will probably still whine about having to go though the MSQ anyway, cut quests or not.
Considering how long it took the devs to implement even the most basic features like right click RMT reporting, allowing people to use the DF with a chocobo, and using egi glamours, I think the whole "gut quests I don't like" would pretty much bring almost everything to a halt. This is the deck we are being dealt and I don't see anything changing anytime soon unless the devs suddenly got an expanded team or an even larger budget for upgraded servers. Until then, we are going to keep getting shortcomings and band aid fixes and no amount of "cut fetch quests pls" is going to move this stubborn mountain no one likes.