*Runs into this thread meowing loudly because this is a subject matter that I am emotionally invested in*
So there are already a number of tabletop RPGs based on Pokemon. Majimonsters. Familiars of Terra. There's even a Pokemon fangame! Thing is, all of these games are really your bog standard fantasy adventure game where every player is the Ranger Class and has an animal familiar who works very much the same way animal familiars do in any old fantasy adventure or dungeoneering game.
Are you hoping to make another one of those? Or something different? What would or wouldn't work really changes based on those kinds of decisions I think.
I'm really interested that you mention 'focused around a bestiary' in particular. Because the 'study' aspect of Pokemon and other collectible monster shows and games is really underutilised in my opinion.
And you mention that a game where you play as a monster trainer would probly have to have the most amount of bookkeeping. I don't think that's necessarily true. It definitely is if you want to have a pre-written list of monsters with all the qualities and abilities they have, and you want to create an immersive open ended play experience that allows players to explore any and every aspect of being a monster trainer. But not so true if you focus it down. Center play on one specific aspect of being a monster trainer. Or go the Let's Go route and give the players one specific starter monster that the game centers around.
Honestly, I'm a bit disappointed that Pokemon Sword and Shield is bringing the three starters back just because it means we now know that there will be less interacting with the starter pokemon! I think the same applies to tabletop design. If you give the players fewer monsters to choose from, then that might appear more limiting on a surface level, but it allows for greater scope of play with less design work from you and less rule management/setup from players.