There might be a fanfiction where Fluttershy befriends a new student in the Equestria Girls school who is also very shy. They help each other come out of their shells and form a strong friendship. This could involve them doing things like joining a club together or standing up to a bully.
To write a good Equestria Girls Fluttershy fanfiction, you should also consider the setting of the Equestria Girls world. What's the school like? How do the other characters interact with Fluttershy? You can create some interesting interactions, like a conflict with a more popular girl who misunderstands Fluttershy's shyness for snobbery. Then, resolve the conflict in a way that shows Fluttershy's kindness.
Another characteristic is her connection with nature. Fluttershy is often shown having a deep bond with the forest and all the creatures in it. In many fanfictions, she can communicate with animals in a special way, and she uses this ability to solve problems or just to have a peaceful coexistence with nature. This connection makes her a unique and interesting character in the world of fanfiction.
The main characters are likely to be the Equestria Girls themselves. Twilight Sparkle from the human world would be a central figure as she often takes the lead in many situations. Then there are her friends like Rainbow Dash, Pinkie Pie, etc. Also, the pony versions of these characters might play important roles as they interact with their human counterparts.
Spike may develop more confidence in expressing his emotions. As he falls in love with Fluttershy, he might become bolder in his actions and words. Fluttershy could become more outgoing as well. With Spike's love and support, she might find the courage to speak up more often and be more assertive in certain situations.
One interesting plot point could be the culture shock the Equestria Girls experience when they first arrive in Equestria. They might be amazed by the magic that is so commonplace there but strange to them. Another could be their interactions with the ponies. For example, they might have to learn new ways of communication and social norms.
Fluttershy and dragon fanfic often explores unique relationships. In many such fanfics, Fluttershy's gentle nature contrasts with the powerful and often mysterious nature of dragons. It can show how Fluttershy's kindness might tame a dragon or how they form an unlikely friendship. For example, Fluttershy could use her understanding of animals to communicate with a dragon in a way others couldn't.
In these stories, Fluttershy often becomes more confident. Taking care of a baby requires her to be assertive and make decisions, which she may not be as used to in her normal life. So she grows in her ability to lead and take charge.
The tree could communicate with Fluttershy through the rustling of its leaves. Each different pattern of rustling could convey a specific message or emotion. For example, a gentle, slow rustle could mean the tree is happy, while a rapid, sharp rustle could indicate danger. Fluttershy would have to learn this unique language, which would deepen their bond.
One great MLP Fluttershy romance fanfic is 'Fluttershy's Heart's Desire'. It has a really sweet plot where Fluttershy discovers her feelings for a particular pony in a very natural way. The writing is good and it stays true to Fluttershy's character.