In the foregoing two Series of Essays we developed a Substance-Accident Metaphysics. We considered classical texts in the Classical Series of Essays, and proposed an update of this Metaphysics based on dynamical systems theory and mereotopology in the Non-Classical Series of Essays.
But this Substance-Accident Metaphysics is still not without problems :

It holds that Reality consists of a multitude of subsistent things, that are discrete from one another and more or less independent. They are concrete "Substances", which means that each Substance is an individual entity, determined by a complete set of determinations. Some of these determinations are "essential determinations" which means that they reflect the very (specific) Identity or Whatness of a given Substance. Other determinations are just occurrent entities, they can be replaced by other determinations without thereby changing the specific Identity of their Substance.
But it is hard to objectively assess the ontological status of occurrent determinations and permanent determinations without involving a stipulation that draws an ontological dividing line somewhere within the class of permanent determinations, separating ontologically dependent (auxiliary) determinations -- dependent on a subject (substrate), like the occurrent determinations, from determinations wholly and intrinsically belonging to that subject (substrate).
To express this more precisely :   Some permanent determinations (like the ability to laugh in humans) are supposed to have the same ontological status as do have replaceable determinations, and are in this respect equated with occurrent determinations. Other permanent determinations (like the ability to think in humans) are contrasted ontologically with occurrent determinations and interpreted as essential determinations and as such belonging to the Essence of the thing and appearing as differentia in the definition (for example as rational in rational animal). In addition to this problem, which has already been discussed earlier, there are other problems as well :

That many things, including complex things, possess something like an "essence" or "nature" is the main topic of the Substance-Accident Metaphysics, but also its main problem. The Substance-Accident Metaphysics assumes "natures" (essential parts), persistent in things from many different classes, including complex things like organisms. This philosophy is indeed inspired by (features of) organisms, especially human beings, i.e. inspired, among other things, by our (experience of our) self-consciousness. We experience a certain continuancy under changing conditions, and this experience is somehow laid down in our language, namely its (explicit or implicit) subject-predicate structure.
But organisms, including ourselves, are complex entities, that in some way are generated, through self-organization of more primitive entities into more or less stable patterns. These primitive entities in turn are generated from even more primitive entities.
So such complex entities, like organisms, appear to be not fundamental at all, but derived. Hence maybe only the smallest most primitive entities are (the ultimate) beings all by themselves, while their complexes are just patterned aggregates of those ultimate entities, having just a derived identity or essence. So the only entities that really exist all by themselves -- that are the very real beings, beings, having a self -- appear to be those ultimate constituents. But these ultimate constituents do not seem to have the nature of "things" anymore. They seem to have a dual nature :   sometimes they are particles, sometimes waves. Or maybe both pictures -- particles and waves -- are inadequate images of them, and thus reflecting their nature of deficient beings.
Hence, where we do find things, they seem to be not fundamental (things), and where we find "the fundamental" there we do not find things.
So it could be that there are no subsistent fundamental things, each having its own specific identity (Essence), after all. And this means that a Substance-Accident Metaphysics would be obsolete. The cause of the popping up of this problem stems from the fact that in those days, in which this Metaphysics was founded and developed, any idea of dynamical derivation and development of complex entities from simple entites was absent, resulting for example in the view that each organic species was something fundamental and original. Now we know otherwise. We live in an evolving world.
The Universe could be completely continuous and moreover totally dynamic, where "laws" could be no more than more or less unstable "habits", which means that there are no genuine constant "natures", "essences", or specific identities. Those "natures" then are fuzzy, and consequently also the "natural laws" that derive from them. If there is some constancy in Reality then this could only be temporarily so, or, that constancy is in fact only a quasi-constancy, randomly fluctuating within a small undetectable range of values. But while in this case empirical science still remains possible, a Substance-Accident Metaphysics is not.

Further, we know that a Substance-Accident Metaphysics is based on a Realistic Theory of Knowledge (See the Essay on The Realistic View of Knowledge). This theory could turn out to be wrong, or, only -- in a way -- valid for macroscopic reality, i.e. only approximately valid.

Another problem with the Substance-Accident Metaphysics (as it is treated of on this website) is the well-known Mind-Body Problem.
In many philosophies it is presupposed that the ontological constitution of MAN is fundamentally different from that of animals, and from that of the rest of subsisting things. It is presupposed that a human being is constituted of two relatively independent "constituents", namely body and mind. While the human body is assessed to be ontologically equivalent to all other macroscopic things, the mind is supposed to be completely immaterial and more or less independent of the body. In this way a new type of entity enters the domain of Reality as soon as human beings come into the picture, i.e. when they are being ontologically assessed. A human being should accordingly be something quite different from being just a dynamical (dissipative) system of great complexity. And this would imply that our dynamical systems approach would not enjoy complete universality. Even worse :   The very instance of a BEING could not be exhaustively (ontologically) evaluated and described by our theory of beings as products of dynamical systems.
We shall address this problem in one of the Essays of this Series, and see if there is a solution at hand.

Further we face the Problem of Individuality.
A Substance-Accident Metaphysics is dependent upon a certain specific view of what it means to be an individual. There are two main types of "an individual" (individuum), namely the here-and-now individual and the historic individual. While in the former case we consider a Substance only at a definite point in time, the latter considers the whole succession of states, that a Substance goes through, as representing the individual. Only this latter view is compatible with a Substance-Accident Metaphysics. So we must investigate whether such a view of individuality is correct. And that means that it should also apply to inorganic beings.

Finally we should deal with the Nominalistic Philosophy.
Nominalism does not in any way recognize "natures" or "essences". It holds that such entities only result from our way to gain knowledge. In Reality there would be individuals only. We shall deal with such a philosophy in one of the Essays in this Series.

So it is certainly not established that the Substance-Accident Metaphysics is the one and only Metaphysics, underlying all of Reality.
The following Essays are going to deal with the mentioned problems, in order to provide some legitimacy for a Substance-Accident Metaphysics.

Of course many problems and possible inconsistencies relating to the very possibility and veracity of Substance-Accident Metaphysics are already dealt with in the other Series of Essays (the Non-classical, and the Classical Series), because such problems already belong to (that) Metaphysics.