I think calling the story and characters of X amazing is inflating things quite a bit. I didn't find any of them that interesting and I can't even remember any of the affinity missions. I also value cinematic, choreographed cutscenes in Xeno games to deliver story over a bunch of characters standing around like stiff mannequins with stock animations. It's obvious where most of the budget went: its world and systems.

Takahashi himself said they distanced themselves from having an epic, theme-laden story with X because their focus was on implementing the necessary tech needed for HD development since it was their first HD game.

The side quests were pretty cool but lore isn't story.