@warbird  

 
The Pokémon are not meant to be representative of their pets, but just what kinda fits their personality, traits or just in general “what you first think when you think of this character”. Pinkie has Psychic “Bounce Pokemon”, Spoink. Fluttershy has a small Normal bird, Starly. Only Rainbow Dash has one that is very reminiscent of her pet. For the same reasons why she ended up with Tank in the show to begin with.
 
For the rest of the cast, there won’t be a Pokemon because the ones I feel fitting for them, would take too much space.  
But just in case someone is interested what I feel to fit them:  
Twilight: Galarian Ponyta  
Applejack: Growlithe/Riolu  
Sunset: Torchic/Cyndaquil  
Rarity: Sylveon/Flabébe/Spritzee

 
I found all the playable characters the boys and the girls from Pokémon games

I’m so glad you finally got around to Rosa, super cute. But why didn’t you give Pinkie a sandile or totodile like Gummy?
 
I mean you give Rainbow a turtwig like Tank. Also curious why you didn’t give Fluttershy a buneary to replace Angel bunny.
 
I have to assume that Rarity will have a pokemon with a gemstone like Staryu, Starmie or Sableye.

Good morning sapphire rarity is last who’s gonna the last Pokémon girl