I think EP6 is my favorite so far just because of how easy it is to understand. EP 1-3 felt pretty disjointed and felt pretty hard to follow because it just seemed like a bunch of different things happening at once. I still don't quite understand why Matoi is so important to our character even after it all.
This is an unfortunate side-effect of how the story originally was for EP1-3 in JP - matterboards. Besides the essential chapter story quests you played through, there were matterboards you had to complete to a certain minimum with various cutscenes, fighting random enemies a certain amount of times for a drop, etc. There were very few requirement to proceed short of filling the red nodes on the matterboard with numerous side cutscenes and such. When they turned them into what's called 'omnibus' quests, they sort of took out most of the pointless side cutscenes, kept the important ones, and threw them into the original story quests. These omnibus quests are what NA now has as regular story mode, and was also incorporated as the regular playthrough for story on JP as well later on right before NA came out.