You could portray their relationship as a rivalry that turns into a grudging respect. For example, at first, they compete for resources or the best missions. But then, when they see each other in battle against a particularly tough kaiju, they start to respect each other's skills.
Perhaps make their relationship based on a mystery. They seem to have a connection that neither of their pilots fully understand at first. As the fanfic progresses, it could be revealed that they were both part of an earlier experiment or something similar that ties them together in a deeper way than just being jaegers fighting kaiju.
Maybe a fanfic where the pilots of Gipsy Danger and Striker Eureka swap jaegers for a mission. This could lead to some really interesting character development as they have to adapt to the different machinery and learn about each other's usual roles in a more hands - on way. They could also discover new things about their own jaegers from this experience.
One unique way is to make Bumblebee and a Decepticon character have a mentor - mentee relationship in a reversed way. Maybe a Decepticon who has been around for a long time and has seen a lot can teach Bumblebee some valuable lessons about survival in the war - torn world, not because he wants to help Bumblebee but for his own amusement. And Bumblebee, in turn, starts to understand the Decepticon better.
One unique way is to show their relationship as a spiritual connection. In the fanfiction, they could be two sides of the same coin, representing different ideologies but also being linked on a deeper, almost metaphysical level. They might have shared dreams or visions that they initially don't understand but later realize are a sign of their connection. This could lead to some very interesting interactions as they try to figure out what this connection means for their war.
One unique way is to give them a shared hobby. Let's say they both love to paint. Hades paints the dark and gloomy landscapes of the Underworld, and Persephone paints the vibrant and colorful scenes of the mortal world. Through their art, they understand each other better. Also, you could show their relationship as a bit of a role - reversal. Maybe Persephone is the more assertive one in the relationship, and Hades is the one who is a bit shy and reserved. And for a more complex portrayal, you could make their relationship a bit of a mystery to each other. They keep secrets from each other, not out of malice, but because they are afraid of how the other will react, and as they gradually uncover these secrets, their relationship deepens.
In a more action - packed way, their relationship could be portrayed as a sort of 'yin and yang'. Jazz is quick and nimble, often taking risks that Optimus Prime might not initially approve of. But over time, Optimus realizes that Jazz's boldness is what the Autobots need sometimes. And Jazz learns to respect Optimus's more cautious approach. They balance each other out in battles and in decision - making, creating a unique dynamic.
You could portray their relationship as a mentor - student dynamic in a very strange way. Murdoc, the more experienced one, tries to teach 2D things, but 2D has his own unique take on things which constantly surprises Murdoc. They grow from this exchange in unexpected ways.
The relationship can be unique if the male reader is a villain at first. Supergirl tries to reform him. Through her kindness and understanding, he slowly changes. Their relationship goes from enmity to a complicated attraction. It's different from the usual hero - civilian love stories.
One unique way to portray their relationship is through art. Harley could be an artist who uses Ivy as her muse, painting her among her plants. And Ivy could see Harley's art as a way to spread the word about the importance of nature. Also, they could have a relationship based on mutual healing. Harley helps Ivy open up more to people, and Ivy helps Harley find a more peaceful side within herself by connecting with nature. They could go on hikes together, and Ivy would teach Harley about the different plants and their uses, and Harley would share her wild stories with Ivy, making their bond stronger in the process.
Their relationship could be portrayed uniquely by focusing on their cultural differences. Naruto, being a shinobi, has a set of values and beliefs based on the ninja way. The Fem Kyuubi, as an ancient and powerful being, has her own perspective. For example, Naruto might value teamwork and loyalty to the village above all, while the Kyuubi might be more concerned with her own power and freedom. By highlighting these differences and how they overcome them, it makes their relationship more interesting. They could teach each other new things, like Naruto showing the Kyuubi the importance of friendship, and the Kyuubi teaching Naruto about the secrets of her chakra.
Their relationship could be portrayed as a kind of mentor - mentee thing at first. Poison Ivy teaching Harley about the power of nature and how to use it. Then it slowly turns into a deeper friendship and more of an equal partnership.