Some of those things are due to how little the game explains itself, but other things I discovered through finally checking out the Xenoblade Wiki and reading fan theories. I guess the two are similar, because even the main story itself isn't fully explained in its own cutscenes. But from my reading, I've decided two things: 1) Elma is awesome once you really dive into her back story and 2) wow, does Xenoblade Chronicles X need a sequel! I've wondered for a long time why people are so hopeful for a sequel. I mean, I know the story ends on a huge cliffhanger, but I somehow never got "needs a sequel" vibes...until now.
Anyway, I'm the type of player who wants to experience a game in as organic a fashion as possible. I don't often look up answers or strategies, but I honestly recommend the opposite for any new Xenoblade Chronicles X players, if such people exist. Start by looking up gameplay tips, especially about the combat and other systems. Get through the main story before looking up characters and other plot-related elements. That's what I've been doing only recently, and I'm suddenly seeing new connections and old connections in a new light.