See how everything pops because of the contrast between light and dark? It shows form, the shape of the subject matter. Simply put, it "pops" from the page.
Go pick up a good art book at your local library and read up on shading and basic art techniques. One must master (or at least get the hang of) drawing before taking on pixel art or any sort of digital art for that matter.
How does one make something non flat? D:
its kinda flat dont you think?