So, for a uniform electric field, or plane electromagenetic wave, if you use a cube instead of a sphere, you can visualise that what goes in also comes out. For the sphere, you can visualise it as being made of many cubes of many different sizes.
How about if the sphere encloses a single charge, and there are no charges anywhere else? The flux is always equal to the charge within the sphere (it's true even if you have an arbitrary distribution of charges outside the sphere, but then it's harder to visualise why, because there is no spherical symmetry in the electric field within the sphere). If you increase the area of the sphere by increasing the radius r, the flux should stay the same. since the bigger sphere encloses the same amount of charge as the smaller sphere. How do we visualise this? The area is proportional to r^2, but by Coulomb's law, the electric field is inversely proportional to r^2, and compensates exactly for the increase in area. This wouldn't work if Coulomb's law contained the inverse of r^3, nor would Gauss's law be true then.