> Why does it use green for both Probability and Algorithms? Why does it use red for both Linear Algebra and Others?

I don't know very much about variations in human color perception, but to me at least, all the colors are clearly distinct (Algorithms&Complexity is a light blue (cyan perhaps), and Others is a sort of pink/purple (magenta perhaps).

> Why is it 3d?

Why not? Don't be so serious!