I think your concept and narrative are really beautiful and vibrant. The greater focus on the characters and how their journey affects their setting is potentially interesting and poignant, but if you bolster the environmental impact on the world and the bees (maybe through gameplay extending beyond pollination of the flowers and showing how it changes the environment over time), it will emphasize the themes surrounding climate more strongly.
My biggest concern that jumps out is your scope. This is a very ambitious project and I am impressed with what you have come up with. However, I'm not sure that a month and a half will be enough time to make the full game you put forth in your GDD, with all the art, gameplay, and narrative elements you want to include to make your game what you want it to be.