There are several uses of Pointed as a separate beast from Applicative. In particular it comes up when we talk about "affine traversals", and would let us refine the type hierarchy of lens, so you'd think I'd be for it.
However, to move it into its own class would require literally everyone who currently has an Applicative instance to clutter their code with CPPs.
Even as the author of the Pointed class, I personally find that the benefit of the change doesn't warrant the impact of the change.
-Edward