@Shadex The Matterboard (the way the story originally played out) was not friendly to those who played in multiplayer groups because so much of the context-based story in Episodes 1-3 involved finding the right areas, fighting the right enemies, getting certain enemies to spawn, getting certain drops to occur, and finding relevant areas around the lobby to trigger the scenes. All of these pulled you out of your party and griefed other players you were with because you would be dead weight in the parties (or would be outright removed) and forced to start over to find the next part. When it came to the bigger fights like the Emergency Quest-related fights your story progress hinged entirely on following the Emergency Quest schedule and having players to help you because you otherwise would have to solo those fights (which were very hard at the time).
In Episode 2 the player is introduced to the Matterboard which allows players to complete a checklist of scenes in order to move on in the "larger" story and introduces dead ends to the story that requires players revisiting parts of the story to retcon paths to find their way forward in the story. On paper this sounds like something every other game would have done for story progression but its implementation in Phantasy Star Online 2 was tedious, lackluster, and heavily convoluted to the point where Episode 4 and 5 replaced the Matterboard with the "Omnibus" instead. Later on in Episode 5 this was completely scrapped out so you purely get the story and then relevant (and curated) versions of the boss fights without having to grind and hope for the chances you get the correct circumstances.
Episode 1 is a very big baggage of "here is a world where everyone talks about the past but won't tell you about why it matters" shotgunned to the wall over and over again with so much filler until the very end when something "had" to happen to end the episode. Episode 2 starts to get more clear with its path (because it retcons Episode 1 via time travel magic) and Episode 3 starts to solidify what Episode 2 was about. When you play through Episode 5 (which is a semi-reboot of what established Episode 1) you will have a much clearer idea of what Sega decided to settle on for the Episodes 1-3 story in the long run. The anime series does not completely tie in nicely to the actual game due to it omitting several Episode 3 aspects of the story (which then make it so Episode: Oracle cannot have the events of Episode 6 playing out due to those story elements being omitted).
The story really could have been handled more nicely and smoothly, I would agree. But unfortunately for Phantasy Star Online 2 you are better off taking the story not so seriously until you get towards Episodes 2-3 or Episodes 5-6 (or Episode 4 if you really wanted to detach yourself from the Episode 1-3 story).