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.
The chronological order can be a great way to read the Shadowhunter novels. However, some people might find it easier to start with the most popular ones first, like 'City of Bones'. But if you want to really understand the backstory and how everything began, you could look into pre - quels first. For example, 'The Infernal Devices' series which gives a lot of background on the Shadowhunter world and is set in an earlier time period. After that, you can start with the main 'The Mortal Instruments' series in order.
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.
Well, as far as I remember, it might have been 'Tobias' Hidden World'. But you might want to double-check in some dedicated Shadowhunter forums for a more accurate answer.
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.
Well, one way it could work is by having Hermione's love for knowledge translate into an interest in the Shadowhunter world. Maybe she stumbles upon some Shadowhunter lore in the Hogwarts library. Since she's always eager to learn, she becomes a huge fan. She could start comparing the magic in the Shadowhunter universe with that of the wizarding world, like how their runes are different from spells.