That's a good point. I decided to lower the alpha of the shadows from .35 to .25. They still look nice, even though they are "brighter".

Btw: I added a screenshot of my menu a while ago (sorry for the german text, I forgot to switch to the english). What do you think about the menu buttons? The color is currently just white and red if the mouse is above. Is that enough or should I add a button behind the text? Maybe a brown button or something.

Hi,
somehow I managed to get the fake 3D right regarding the shadows.

What do you think?
Explanation of what I did:
In GameMaker I used blending functions and surfaces to create that effect.
First, I had to draw all the objects, where the shadow of the clouds shall be projected on, on a specific surface - which I called shadow_surface_objects. Then I draw the cloud shadows on another surface - shadow_surface - with an y-offset of -10. The key to get the result was to find the right blend mode. Currently, this line does the magic: gpu_set_blendmode_ext(bm_dest_color, bm_one - bm_src_color);
By using this mode, the shadow_surface_objects is drawn above. Now, only the intersections between the objects and shadows are drawn.

Thank you for the feedback!
I am drawing my shadow on a specific layer between the floor and the tiles / instances. I will try to hue-shift it to blue (or something like this).
As I am using GameMaker, I draw all the shadows (except the clouds) on a surface. After that, I draw the surface with an alpha of 0.35 on the specified layer (hopefully, I can hue-shift it right here). I was not sure if I should use the soft cloud shadow or the solid one. Booth of them looked good to me. But I will change it to the solid one.

Faking the 3D shadow is not that easy I guess. Sure, you may have the information, how high your object is, but how do you shift the shadow upwards?

My setup is this:
Every frame I draw the shadows with rgb(0,0,0) on a surface. The shadows of the characters is basically the character sprite with slight modifications (stretched). The shadows of the blocks is simply an additional sprite.
So I end up with a transparent canvas with black shadows drawn on it. I think at this point, there is no way I could shift the shadows (in this case the black pixels) upwards. Hopefully, I am wrong and there is a way

Otherwise, I'll just let go of the "cloud shadow".

Lastly, I don't quite understand what you mean with "overlap UI elements". Could you please provide more information regarding this?

Hi,
the thing is, with drawing every single leaf on the branches, that the tree looks kinda naked.

As you can see, the sakura tree is much fuller.
Maybe you could take a look at this: https://www.pinterest.at/pin/519039925792688682/. That is a short tutorial on how to draw trees. Helped me a lot regarding pixel art trees.

Awesome character design! The colors fit pretty well in my opinion.
For the left version, you could add a little bit of shadow where the wrinkles are, just above the hand where there is one pixel missing. Adds a bit more depth.