I'm more invested in Xander when it comes to fanfic.
1) The theme of gender reversal is presented in many of Xander's storylines on the show, but was never dealt with in the same depth as fanfics. I would like to see Xander deal with being raped by a woman (that woman being a slayer (Faith) or even Buffy while under the spell in BB&B) and see how different it's taken when it's a guy.
Link to fics dealing with the aftermath of the episode Consequences.
2) Body switch between Xander (who wishes he was special) and Buffy (who wishes for a normal life.)
Put Yourself in My Shoes
3) I read a lot of Spander fanfics and it upsets me how Xander and Spike have so much in common and yet the show never explored that. I love the idea of Xander's father finding Spike in the basement and kicking Xander out of the house, and both Xander and Spike find another place to live. (Xander doesn't have to end up being gay, but I would like to see him and Spike connecting and perhaps becoming friends.)
Sidelines
4) Girl Xander! Xander turned into a woman for an episode would have been amazing!
When Xander Harris Was a Girl
5) Jesse! Almost all fics, even not Xander centric fics, acknowledge that Jesse existed and that his death was traumatic for Xander. I would have loved to see Xander deal with telling Jesse's parents about what happened to him.
Letters Never Sent
6) Xander dealing with losing his eye. Xander wasn't allowed to mourn his loss on screen because of the apocalypse. I would have loved to see how this injury would have affected his life.
Beholder
7) Giles begrudgingly adopting Xander. What if Xander is physically abused by his drunken father (signs being more clear since S1) and social services get involved? A storyline with Xander and Giles living together reluctantly and slowly growing like one another (in a father/son way of course) would have been amazing to see. I can just imagine how Giles' influence would get Xander more interested in school.
Sands of Time