intuitively, off the top of my head i'd say it's, mmm, focus on two (rarely more, even in gen fics) protagonists and their relationships, with the assumption that the reader knows the context of their relationship with the world around, and everything else - worldbuilding (even in au fics with pretty intricate one), relationship with other people, plot, any kind of message - is done as a backdrop and is... i don't know how to formulate it, markedly less weightly. it's not a writing quality question, just the way of putting accents.

or, alternately: 90% of fanfiction is, mmm, kink-related (not necessarily in sexual sense). say, hurt/comfort fic can be novel-lenght, have intricate plot and multi-cast, and yet it's ultimate goal would be evoking certain set of emotions - and thus would differ from, say, fantasy novel where protagonist gets injured at some point. or: fanfic usually works with emotional plot (setting - conflict - resolution) rather than event-oriented one.

it's all very hard to formulate, i'm afraid :)