Ok, for my Gym Leader line-up in my story, I have hand picked Pokemon for them that represent their personalities, where they live, their abilities and all other things that represent them. For each Gym Leader, I have chosen the following these Pokemon for these reasons:
For Fox, I have chosen Vulpix and Ninetales because they are both fox Pokemon. Does it get any more obvious than that?
For Mario, I chose Bellsprout because of the plant life being highly important in the Mushroom Kingdom, Parasect because of the mushroom on its back represents the Mushroom Kingdom and Marowak because it somewhat reminds me of Dry Bones
For Kirby, I picked Staryu because of its symbol being a star, Jigglypuff because they're both round puffballs and Ditto because it can change its form, somewhat like Kirby
For Capt. Falcon, I chose Spearow and Fearow because they are both bird Pokemon, which are much like his alias being the name of an actual bird
For Link, I selected Shellder because he started his adventure small and its shell somewhat represents his shield, Sandslash because of its arms that can slash things like his sword, Scyther because its arms are blades, which is perfect for him and Dodrio because of the 3 heads representing the 3 triangles of the Triforce, the symbol of Hyrule
For Donkey Kong, I picked out 4 fighting-type Pokemon to represent DK's boastful strength. There's Primape because of its an ape Pokemon to represent DK being an ape, the others are Hitmonchan because of his abs are represented by the punching fiend's signature arm-based attacks and Machoke and Machamp because they are both big and burly like DK
For Samus, I picked Voltorb because of her Morph Ball ability which releases explosives, Magmar was something my brother suggested and I stuck with it because it represents a handful of her attacks and Dragonair because it is as elusive as her
For Ness, I picked Doduo because like Ness, it appears normal but has special abilities, Pikachu because the name PK reminds me a lot of Pikachu and Kadabra because it is psychic, much like him
If you have better suggestions for these characters of what Pokemon you think they should have, please let me know. I might be able to become inspired by your ideas, or maybe offended. Either way, it is what it is.