As in, parts of the story that don't add in to anything yet.. and are just kind of there as extraneous information. Just off the top of my head:
-The "Artifact" at the rescue camp is just kind of there.
-No explanation of where sealed sword/divine avenger/gran faust/valkyrie type stuff comes from other than just as "heaven"- Is this a place? Are there still angels?
-Herex/the rest of the crimson order and it's relationship to the swarm is not fleshed out entirely.
-How does Margrel, the book of grey feathers, and the owlites relate to any of the other major tangents?
-Graviton vortex isn't from any culture?
-Who built the statues and fountains found in wolver dens?
-Where are jelly cubes from? We know where lichens are from, are jelly cubes the same?
-And of course, The Core: The Path Is Sealed
Good notes. What about the ancient astronaut suits in Ghosts in the Machine? Are they explained?
Threads about the story/plot/lore come up occasionally. It would be nice to have a concerted project to improve Category:Lore on the wiki.
It would also be nice if Three Rings took a little time to actually flesh out the plot of this game. I understand that Three Rings is a small company that can generate new levels, monsters, items, artwork, etc. only so quickly. Those tasks take a lot of work to create, test, balance, debug, etc. But it seems to me that they could pretty easily write up a coherent plot for the game, and keep it largely secret, but dole out a little bit with each update. They did this nicely with the Shadow Lair Echo Stones. They need to do it more often. It would help keep players interested in the game, and talking about the future of the game.