I have seen this answer from a lot of people.
1. You don't have to do the whole story, and all the quests just do enough to finish the game, you can skip all the requisition stuff, and sell everything, except the Monster study items, all you need is enough power for the main quest.
I know they mean well, and they may be right, but I payed for an RPG game, and I intend to complete every thing in it at least once. To me anything less is not even playing the game, its just finishing it, which to me seems to leave it un-finished.
I like RPG because I have to explore, and figure out all sorts of things, and that is part of the fascination of an RPG for me, if I don't do all these thing's, then I might as well be playing an FPS. Moving from level to level until I beat the boss, just as fast as I can.
Just my opinion, and I know many who just want to see the end real quick will say it is wrong, and they fully intend to go back, and try everything else out latter. I just have never done RPG's in that fashion.
I think of it like a book, sure I could just read the first chapter, and then skip to the middle chapters, and then the last chapter, and Probably be okay, but I would rather not skip pages like that.
2. The Op has a point in that Many of the side quests do seem to be dis-jointed from the main quest, and I guess don't have to be done.
But I feel obligated to try and finish them all.
Call me a completist if you want, but I don't think that is a bad thing.