Another possibility is Aquarius. She is a celestial spirit, and celestial spirits have a kind of otherworldly and powerful nature. Aquarius has a strong personality and her own set of powers. If the fanfiction is about a character who has a special bond with Aquarius and has been helped a great deal by her, then she could be the 'My Goddess' that the title refers to.
The fanfiction might be special because it combines two different concepts, Fairy Tail and the idea of a 'My Goddess'. It could bring in a new aesthetic to the Fairy Tail world. Maybe it has a different art style or a new set of magic rules inspired by the 'My Goddess' concept. Also, it could explore themes like gratitude in a more profound way, as the title 'Thank You, My Goddess' implies. This might make the characters more relatable as they express deep - seated emotions towards this goddess figure.
Natsu could be one of the main characters. His brash and adventurous nature would make for an interesting contrast with the more mysterious and powerful goddess of time. He might initially be skeptical of her power but then come to rely on it.
The goddess could be a new character created specifically for the fanfiction. Maybe she's a being from an ancient magical civilization that has been dormant for ages.
It could be a completely original goddess created just for this fanfiction. Maybe she is the goddess of a forgotten element, like the goddess of lightening that has been long forgotten in the ninja world, but still holds great power.
It could be Aphrodite. Given her domain of love, it would be an interesting take. Percy might be charmed by her beauty and grace, and they could end up having a child. The child might inherit Aphrodite's charm and Percy's courage.
The goddess could also be an original creation for the fanfiction. A being with a unique set of powers like the ability to control time and space. This goddess could be betrothed to Harry to stop an impending doom that threatens both the wizarding and Muggle worlds. Her powers would be so great that she needs Harry's connection to the wizarding world to fully utilize them and save the day.
It could be Athena. Athena is known for her wisdom in Greek mythology. She could pass on her wisdom to Harry, making him not just a powerful wizard but also a very wise one. He could use this wisdom to solve problems in the wizarding world in a more strategic way.
The goddess could be an ancient Celtic deity. In the fanfiction, the author might choose a Celtic goddess because of the rich magical lore associated with them. For example, Morgan le Fay from Arthurian legend could be reimagined as a goddess in this context, and she could adopt Harry due to her interest in powerful magic users.
She could be an ancient Forerunner who has been in stasis for millennia. The Forerunners were extremely advanced, so it would make sense for one of them to seem like a goddess with their technology and knowledge.
It could be a goddess of the moon. In Naruto's world, the moon has significance, and a moon goddess could be attracted to Naruto's bright and determined spirit. She might come down from the moon in a human form and interact with Naruto, leading to the situation where she gets pregnant.