The problem is still IME, WP/VP systems are too easy to utilize to bypass HP entirely, leading to certain classes and certain builds becoming excessively powerful.
In HERO, which has such a system, you can target Body (wound points) with certain kinds of attack...but most still do Stun (vitality points). They are balanced by the Killing attacks- the ones that target body- being @3x the cost of normal attacks.
Furthermore, defenses exist against both kinds of damage, which may be integrated or discrete. IOW, characters may be more vulnerable to one kind or another type of damage, depending on build.
They even heal at different rates.
Its not an insoluble issue.