You can make it unique by changing the setting. For instance, if Ash starts with a Bulbasaur in a post - apocalyptic world where most Pokemon are scarce. This would force him to find new ways to train and care for his Bulbasaur, and also deal with other survivors who might be jealous or desperate for his Pokemon. It would be a completely different dynamic from the original series.
Give the different starting Pokemon a special backstory. Let's say Ash starts with a Charmander that was once part of an illegal Pokemon fighting ring. Ash has to not only train it but also help it overcome the trauma. This adds depth to the story and makes it stand out. He could meet other characters who were involved in the fighting ring in different ways, either as victims or as enforcers, and have to navigate those complex relationships.
Change the rules of Pokemon battles in the fanfiction. If Ash starts with a Squirtle and in this world, battles are more about solving puzzles together with your Pokemon rather than just fighting. Ash and Squirtle would have to learn to communicate and think creatively. This new approach to battles would make the story unique, and also attract readers who are looking for something different from the traditional Pokemon battle - based storylines.
Well, you can make it unique by changing the entire personality of Ash based on the starter. For instance, if he starts with a Eevee, he could be more indecisive at first about which evolution path to choose for Eevee, adding an interesting character arc.
One way to make it unique is to have Ash crossdressing not just for fun or by accident, but as part of a prophecy. There could be an ancient prophecy in the Pokémon world that says a hero will appear crossdressed to save the day. And Dawn could be the one who initially discovers this connection. Also, the story could involve Ash having to master a new type of Pokémon training that is only accessible to those who crossdress, adding a whole new dimension to the plot.
One idea could be that Ash starts with a Pikachu that has a rare and powerful hidden ability. This could lead to different battle strategies and interactions with other trainers. For example, instead of the usual Pikachu that gradually grows in strength, this one could be super strong from the start, causing other trainers to be both intimidated and curious.
In a fanfiction where Ash starts in a different region, for example, Sinnoh. He could start with a Pokémon native to Sinnoh like Piplup. His adventure would be shaped by the mythology and legends of Sinnoh. He might get involved in the search for the Legendary Pokémon related to the creation of the Sinnoh region. This would not only add a new layer of mystery to his journey but also expose him to different kinds of Pokémon trainers and their beliefs. His relationships with his Pokémon would also be influenced by the Sinnoh - specific Pokéballs and items available in the region.
You can make it unique by having the spells be tied to emotions. For example, if a trainer is feeling extremely angry, the transformation spell goes wrong and they turn into a half - pokemon, half - monstrous form. It adds an unexpected twist.
Well, it could lead to some exciting plot twists. Maybe he'd have an advantage in battles or face unique challenges because of the variant.
Well, if Ash starts with an Ekans, his team dynamic would be very different. Ekans is a snake - like Pokemon, and it might not get along well with some of the more energetic or flighty Pokemon at first. For instance, Pikachu might be a bit wary of it since they are so different in nature.
Ash would likely become more open - minded. Meeting a shiny ghost pokemon at the start would expose him to a type of pokemon he might not have expected so early. This could make him less fearful of the unknown in general. For example, he would be more willing to explore spooky places or deal with pokemon that have a reputation for being difficult to handle.
Ralts could make Ash more empathetic. Since Ralts is a psychic - type Pokémon that can sense emotions, Ash might become better at understanding the feelings of other Pokémon and people. This could help him in his journey to be a better Pokémon trainer.
He could have a Froakie. It's a common and cute starter in Kalos. Maybe also a Skiddo for traveling across the Kalos landscapes. And a Bunnelby would be a nice addition for its digging abilities.