I absolutely have some go to pokemon, but each also represents something, so I can break them down into how I use them. I write within my own pokemon universe, so all of my stories are the same world, but different times and experiences. Having starters/pokemon that match what that story is about is a key thing.
Going in chronological order I can show you what I mean.
Book 1: Medieval fantasy. themes: Not all heroes are paragons, The knight in rusted armor.
Pokemon choices and reasons: Scyther: a brutal monstrous Pokemon who looks like they exist just to kill. It mirrors the bounty hunter protagonist extremely well.
Book 2: modern fantasy. themes: Doing what you love doesn't pay the bills.
pokemon: charmander: Everyone has a charmander. its so overdone and popular that seeing another character with it is nothing, and thats the point. The character is so astoundingly average in his abilities. he's struggling to be a good trainer. To go pro and be able to be a trainer for a living. Using Charmander shows that he is 1 among millions.
book 3: modern fantasy (modified version of Su/Mo): themes: strength is something we have, but not all choose to use.
Rowlet: definitely the least reasoned of the Pokemon, but the rowlet has developed into an analogy for being two different things on the outside and inside. Rowlet outwardly is this super cute owl Pokemon, but by the time it fully evolves it takes on a whole other existence. It changes into not just something different, but almost something opposite.
book 4: distant future "reclaimed" Apocalypse: themes: A call to duty, is not always a call to arms.
Grovyle: The story actually begins with the MC already well into their life. they are a mid ranking ranger (thus the middle evolution Pokemon). Grovyle itself matches the nature focus of the story, but also is a generally cocky strong willed kind of Pokemon. It helps to explore all the important character's reaction to traumatic events through their life. It also frees the MC to feel a bit weaker (Since the grovyle is the MC's partner he can be the one who stays strong and tough on the outside while the MC is shown falling apart after the trauma. They still have enough power between them to keep the plot moving, but it still shows the wear of such events)