I don't have a 3D printer but I like the idea of having the resource tray as different tracks so you could get the crop track out according to the season. I'd probably have the crop tracks coloured by seasons.
The farm tray for buildings and animals is also a good shout, I may make a separate board at some point for laying out the farm, for fun or maybe adding some rules/functionality. The animals and buildings would best have fresh tiles shaped and sized accordingly, there'd be somewhere there for gold and hearts perhaps, and possibly 5 crop watering markers so I could plant my crops in my chosen spots on the farm (not sure how hoe power would work perhaps adjacency would be required, the rules I would add would be to have weeds to clear, where items can then land during the season phase if the starting player is full).