I have read and written a handful of MMORPG-based fan fictions over the years. Outside of contests with specific rules, their length and content varied widely. Some followed the official lore closely, while others explored alternate realities or timelines. Some were fairly serious, while others took a comic approach, going as far as incorporating internet-based concepts like lag and chat filters. Fanfic is a way to express yourself – be creative, and don’t let a lack of examples stop you from writing your own!
As for PSO2 specific content...
PSO2’s story mode takes a very meandering path through events, and leaves a lot of room for interpretation. If I were to write a fan fiction based on PSO2, I would probably take one of two approaches:
Approach #1: Dodge the actual events of the story mode, and tell MY characters’ stories the way I want them to be told. The official story is happening to someone else, completely apart from what’s going on in my tale.
Approach #2: Tell the story mode “how it should have been”. The personality I developed for my main character does not always sync well with the cutscenes she takes part in. I think it would be interesting to have a player character “go off script” in the middle of the story, changing the outcome of a critical scene. From there, the tale would take a completely different (and probably darker) direction than the canon one.
Approach #3: Write the memoirs of Dudu. There has got to be a good story behind this guy’s bad luck.
Also, if you haven’t done so yet, I would recommend visiting the PSO-World Forum Fan Works section – it might have some of the inspiration you are looking for.