It's really nice that you bring back 1 hit ko moves and smart how you handle them but my question is, are the restrictions only for boss-mon or for every fight in the game?
Changing the boss battle to something that is more like a puzzle instead of this impenetrable wall is really great... looking at you Hippowdon.
To focus on the Legendary that are important to the story and to give them story quests etc is in my opinion more important than to give every single Legendary a story. I mean there are 82 legendary including mythicals, so even if you would put them together (like bird trio, dog trio etc) there could still be over 20-30 quests depending on how far you would've wanted to go. So in that regard I think your move is a good one.
Art and music are fire as well so all in all really good changes and updates.