I love how so many people ignore the argument of "because of Trusts, it changes the narrative of the game, in one instance nonsensical" and just spout "don't use Trusts then" without even trying to understand the point. Thing is, even if a player were to not use Trusts, said player would still watch the cutscenes in the MSQ, where suddenly Character N appears out of nowhere.
Square Enix needs to write the story in a way that puts Trusts in the general area of the instance, to justify their existence in the Instance. That is the issue OP is pointing out, and I have to say, I quite agree with that stance. Its not that the Trust system is a bad thing, its that it impacts the story in noticeable ways.