>>32574573I'm going to start messing with the roof stuff tomorrow.
As far as the linearity, that cave on Route 2 is going to have an underground waterway that forks. One path takes you to a cave exit at the cape under the berry tree, and the other path will lead to an optional water route to the right that links to a town later in the game. When you get surf later (in that town) you will be able to take an alt path back to the earlier parts (kinda like Diglett's Cave).
>>32574635I already have. The blue flowers in Sunset Bay are using the roof palette.