I think my biggest peeve is a long, 100+kb, story that is posted as one piece and not broken up into chapters or that have long chapters. Some are much too long to be read in one sitting, and are a real mess trying to find your place when you come back the next day, or move to a different computer/tablet. There used to be a feature where SoL would break long stories into shorter chapters and put in a note that the chapter breaks were set by SoL, not the authors. Some of those breaks made for weird reading! Chapter breaks are the reader's friends.
JimQ2