It certainly depends on how you play with and display your Playmobil, but I find Raven's multi-container approach to be quite intuitive. This approach allows you to organize from general to specific, using any categorization system you choose, and can be adapted depending on how much you have of various items. White flowers in a small baggie, pink flowers in another, yellow in another, etc.; all of the smaller baggies go into a larger "flowers" bag; this "flowers bag" goes into a larger container called something like "plants," which could include trees and vines and ferns; the "plants container" could go into a larger "outdoors/nature" container along with animals.
Personally, I find steck pieces a joy to organize neatly into boxes by type.
