I think generally speaking that Yooka Laylee was a fun game, but there were key elements that it lacked which I think could be improved upon should the team venture ahead with YL2 (though I don't think that'll be the next game they make).
I would agree mostly with the characters. I felt that the reason why people weren't clinging too much to the worlds is because there wasn't enough character within them. It didn't feel as though there was much life, like these worlds were organic that each character belonged in and lived their life. I think this is because of a couple of reasons. 1, like mentioned above, each world had the same character with just 3-5 different outfits on (snowmen in GG, shopping carts in MM, slot machines in CC, frogs in GG). There wasn't much variety in them, which just made the experience feel lifeless. And 2, the worlds exist within books. How does one travel from one book to another? What books are we reading/entering? Books are stories, and each world should have a story, characters within it to tell stories, and something to build up to. No character in any of the worlds really had a story to tell (Shovel Knight and the pigs are the closest to this). Which brings me to my next point...
Villains. Each world had a boss, but if we're in book worlds, shouldn't those bosses be villains of each world? Shouldn't they be universally known by other characters, and have more intricate designs? The bosses in YL, while in some ways fun to fight, lacked that life that the characters needed. Better world bosses are crucial going forward.
And yes, I agree the overall story needed more pizzazz. It didn't really make much sense that the book we own and are running after is the one that scattered its pagies everywhere because in the end, when we collect all the pagies, we have our book back. No need to go fight Capital B, right?
I think the expanded worlds were a great idea and really do tie into the book worlds. When a level looks unfinished it's because part of the book is missing. Put the pagies back, the book is complete, thus expanding the world. I would keep that idea going forward, but again, make sure the worlds are really within a book and have a story to them (and characters that exist within them).
So to recap, going forward to YL2, the things I think should be focused on most that would make the game better than the first are story, character, setting, and how they all tie into one another smoothly and organically. Oh, and transformations that actually require you to do more than one thing with them

Edit: I think the moveset worked well in this game, and agree that the flight may have been too easy once you got it. Perhaps put more of a limit on this move because if you go into a second game, wouldn't you already know how to fly? That may be a problem.
And one final thing lol, but the actions that end up changing a world (like making the cloud rain and creating a river) should actually have a purpose. I don't think that river in Tribalstack Tropics was even used for anything...