The problem is that, as we've pointed out, the most glaring issues with the narrative would have only required exposition. That we're constantly asking "Wait, what the fuck?" every single chapter doesn't mean that the game isn't salvageable, they just need to actually explain what's going on.
How to fix Jared: Add a quest where you stay the night at the inn and Jared speaks to you about his time in the Crownsguard (that's what he was, right? Some older Kingsglaive member?) and have the guys sit around listening to him. Hell, this would have been a perfect place to incorporate most of the Dawn trailer. "He was a good man, your father, he loved you." etc, blah blah blah.
How to fix the Summon macguffins: Allow the player to actually acquire that Cosmogony book that is randomly lying out in the open at various locations, have the bros talk about it, explain what a Covenant is, have them go "Luna must be speaking with them to get them on your side ahead of time" or whatever. Say something like "No one knows where Bahamut is" and "Legends say he Ifrit has grown to hate them, and mankind as well." Plant the seed. Make the player curious.
How to fix the Royal Arms macguffins: Simply state that you don't need to actually collect all of them. Make some reference that Lucian kings can be temporarily granted their powers without needing to permanently acquire the weapons in times of great need. Now suddenly finishing the game with only half of them makes a little more sense.
The narrative problems with this game aren't unsolvable. They just required better writers, and unfortunately, a better director.