But also - most of the time gamedev happens in 3D space not in 2D space (even if it gets rendered down to 2D). So it's more natural to do a dot product of two 3d vectors, than try to mess around with trig functions that work on scalar angles. Same with rotations: it's easier and better to use quaternions in 3D space than try to rotate along each axis separately.
[1] GPU intrinsic estimated costs: http://www.fractalforums.com/programming/shader-function-or-...