The game doesn't have an ending yet, I never had the time to implement it.
The action keys changing shouldn't affect your ability to use skills, because you can't rebind the buttons for the skills (the plugins I'm using don't allow for it because they're unfinished - the creator abandoned RPG Maker altogether a couple years ago).
Were there any cutscenes in particular where this happened?
The trees respawn because they are enemies, and because I was planning to allow the player to make more fires but I never got around to it.
The recipes were added as I added things, but yes, some enemy drops went unused because I ran out of time. I have no plans of letting the player craft equipment, the decision to keep the player at one weapon and some armor was deliberate.
The plants aren't supposed to be passable because they are enemies. If I set them as below the player, then harvesting/"attacking" bugs out (the same is true for enemies set to above the player). The bats deal 0 damage half because I never had the time to balance their skill and half because I didn't realize how badly Drifty Mode is unbalanced in the player's favor.
The fairy isn't supposed to be an actual party member, she was never supposed to be. She is accompanying you. As for Teriny, I never had the chance to balance her because I was focusing on the gameplay as Donicus (since you spend most of the game as him).
I am glad that you enjoyed the story, I apologize that there were as many bugs as there are. The bugs and general uncompleted nature of this game are why I plan on releasing a final, finished version after the jam is over (after the winners are announced) - bugs hopefully fixed, some more balancing, more story and gameplay content, and less wonky collision (which was primarily because I couldn't use my mapping system of choice).