Well, Alec as a girl could lead to some comical situations at first. For example, he'd have to get used to different clothing styles and the way society in the Shadowhunter world treats women. Also, it might change his romantic relationships. If he was in a relationship before, his partner might have a whole new set of feelings to deal with.
His character might become more in - tune with his emotions. Often, in society, girls are encouraged to express their feelings more openly, so Alec might start to do the same. He could also become more aware of the gender dynamics within the Shadowhunter world.
Another possibility is that it's part of a scientific experiment that backfires. Xander now has to deal with the social implications of being a girl, like different expectations in school or in relationships. He might also find that some things are easier as a girl, such as getting away with certain behaviors because of different gender stereotypes.
Stiles is a must - have main character. Then, depending on the direction of the fanfiction, characters like Simon Lewis could be important. Since Simon is a vampire in the Shadowhunter universe, his interactions with Stiles, who is new to this world, could be really interesting. Also, characters like Luke Garroway, the werewolf, might play a role, especially if the story involves the relationships between different Downworlder groups and Stiles' place in all of that.
I haven't read Bella's Shadowhunter fanfiction specifically, but in general, fanfictions can be really good. They allow fans to express their love for the original work in their own way. If Bella is skilled at writing, she could have added her own unique spin to the Shadowhunter universe, perhaps delving deeper into the backstories of some characters or exploring different magical aspects.
One idea could be that in this fanfiction, Draco's transformation into a girl might be due to a magical accident. Maybe a spell backfired while he was trying to outdo Harry Potter in a duel. This could lead to a whole new set of adventures as he has to navigate Hogwarts in a different body. He might face new challenges with his Slytherin peers, who may or may not accept him in this new form.
One popular one could be 'Stiles in the Shadow World' where Stiles discovers his Shadowhunter abilities and has to navigate the complex world of Downworlders and the Clave. It has great character development and interesting plot twists.
One idea could be a crossover with the Vampire Diaries. Shadowhunters could team up with the Mystic Falls gang to fight a common supernatural threat, like an ancient demon that neither group can handle alone. This would bring together the different mythologies of the two shows.
Simon Lewis is often a popular character. Since he has a unique background as a vampire who was once a mundane, his perspective and experiences add a lot of depth to fanfiction stories set in the Shadowhunter Academy. He can interact with the students in interesting ways, sharing his knowledge of both the mundane and the Shadowhunter worlds.
There could also be a storyline where the academy is under threat from an outside force, like a group of demons that are specifically targeting the young Shadowhunters in training. The students then have to band together, using their unique skills and the knowledge they've gained at the academy to fend off the attack. This would show their growth and development as future protectors of the Shadowhunter world.