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.
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.
One idea could be exploring the backstories of minor characters in the Shadowhunter Chronicles. For example, you could write about how a particular Silent Brother came to be. Another idea is to create an alternate universe where the Shadowhunters have different powers or abilities. You could also write a fanfiction focusing on a romantic relationship that was only hinted at in the original series.
Yes, there are quite a few. You can start by looking on fanfiction websites like Archive of Our Own. There are many talented writers who have explored the concept of Bella Swan in the Shadowhunter universe. Some might focus on her having the abilities of a Shadowhunter, or her interactions with the existing Shadowhunter characters.
Alec and Isabelle could be important characters too. As part of the shadowhunter group, they have the skills and resources to track down Jonathan. They could be the ones who gather intelligence on Jonathan's whereabouts and plan the rescue strategy, while also dealing with their own personal issues and relationships within the group.
On the other hand, there could be a glimmer of hope in their relationship. Maybe through the shared experience of the pregnancy, they start to see the good in each other. Clary might see a side of Sebastian that she never knew existed, and Sebastian might start to have real feelings for Clary and the baby, leading to a more complex and evolving relationship.
Well, it depends on how it's executed. If it's just a simple idea thrown together without much thought, it might not be that great. But if the author really delves into the differences and similarities between the two universes, like how the magic systems work and the different cultures of wizards in Harry Potter and Shadowhunters, it could be a very interesting fanfic.