The reason is that choosing $a=-3$ allows for a more efficient computation of the doubling operation, when used in projective coordinates.
In fact if you look at the doubling formula in, for example, Jacobian coordinates from wikibooks you can see that it requires the computation of an intermediate value as $M = 3*X^2 + a*Z^4$, where $(X,Y,Z)$ is the Jacobian representation of the affine point $(x,y)$ through the relation $(x,y) = (X/Z^2,Y/Z^3)$.
That formula to compute $M$ can be simplified to $M = 3*(X + Z^2)*(X - Z^2)$ exchanging the computation of two squares $X^2$ and $(Z^2)^2$ with the multiplication $(X + Z^2)*(X - Z^2)$ and, of course, you also avoided the multiplication by $a$.
This results in a more efficient computation of the doubling formula and works well even in homegeneous or Chudnovsky coordinates.