I bet no one will read or care about this... (especially given that the 'audience' is drowning in cynism and have probably completely discouraged Playtonic by now...)
But well, here's a shot in the dark.
I think it could be interesting, actually.
My own personal theory, going with the meta theme of the current game, is that Yooka might be a rookie or failed 90s platformer hero. The kind who was a Sonic-like guy with an attitude, spinning moves, and a disturbingly human-like or human "girlfriend" (who inevitably leave him on the next planned game).
Meanwhile, Laylee would be a regular bat enemy, the type that you see in dozens of duplicates all over the place and are used as completely expendable minions by the bad guy of the week, with no regard to whether the minion survive more than a week or not.
My idea being that Yooka is enthusiastic at first, convinced he's going to save the world and become a great hero only to find out that it's hard work and that he's... not exactly up to the task. In particular, many of his failures might involve a certain bat knocking him down bottomless pits a lot.
With no friendly NPCs to talk to (none that really care or appreciate how hard and painful his attempts at saving them is) and with the odds obviously meaning that he'll never see the end of his quest, Yooka actually do the improbable and try to strike up conversations with the most unlikely of characters, down to the regular bat who knock him down pits.
His desesperation as a hero make the bat feels that he's kind of pathetic as a hero, especially given how out of his league he is. Yet, his sheer determination and willingness to both keep trying and staying idealistic despite the entire game world just metaphorically punching him in the face repeatedly eventually cause the bat to actually talk back.
The bat enemy eventually end up talking aloud about thoughts of its own. How thankless its job as a respawning minor minion is, the knowledge of how certain, sudden, and forgettable its eventual demise is, and how, now that it really think about it, being a minion really suck the big one.
In blatant violation of the initial narrative, the bat enemy decide that it would rather not be a minion anymore and it decide to join Yooka, revealing to him its name: Laylee. Yooka, with Laylee's help, decide to stop pretending to be what he isn't (he just isn't fit to be a high speed 90s platformer hero with an attitude) and to pick his own path.
This eventually allow Yooka to finish the game and save everyone. But instead of going with his alleged 'girlfriend' back to a status quo he realize he doesn't like anyway, he instead leave with Laylee. The newly formed duo now deciding to go on adventures of their own.
It all ends with them settling by a familiar shipwreck, having uncovered a certain book, the two of them planning out their next adventure...
I don't know if anyone will take the time to read this. But if someone does... I hope they will appreciate it. Thank you.