I did not find the hidden caves.
I saw on discord that they were on the cave ceilings. In my playthrough I was very careful about not hitting any walls because the passengers started complaining. So that led me to not find any secrets I think.
I think a game like this would demand manual level design. Because that’s the most fun part for the player. Exploration!
Procedural generation might not be as fun in my opinion.
I understand the time it takes but then that’s almost anything game dev. 😅
I think if you go 3D many things about the game will change and you might need a lot more? Like minimaps and stuff. ( Or do you want to make it 2.5D? Then the transition would be easier. )
You might also need to create more interesting 3D backgrounds to keep the players hooked. 🤔