First, a provisional definition of ontology, gleaned from the Oxford English dictionary and the website “ontology a resource guide”. Not that these sources are definitive, but they do seem to represent mainstream thinking about the subject.

(A) Ontology is the theory of objects and their ties. The unfolding of ontology provides criteria for distinguishing various types of objects (concrete and abstract, existent and non-existent, real and ideal, independent and dependent) and their ties (relations, dependences and predication).
(B) • noun Philosophy: the branch of metaphysics
concerned with the nature of being.

The good news is that ontologies are ambitious because they try to capture all of Being (One might ask, “what is Being?” For our purposes, we can assume “Being = Everything there is”). Therefore, ontologies are one way to grapple with Being as such, not just some domains of particular Beings. The bad news is that ontologies presuppose a distant observer who sees all of Being, a removed God’s eye view of the world. In this picture, Being is the ultimate object of knowledge, and the most basic act of knowing would be to catalogue all there is. Since Being is the ultimate object, its basic property is existence. One can see that this objective conception of Being is reductive, for it reduces appearance, presence, essence etc to one dimension: existence. For example, it reduces the color red to being a property of objects, saying nothing about the way redness appears to a person experiencing red.
More speculatively, we can also see how this conception of ontology leads to one very influential understanding of the goals of science, especially in theoretical physics. A physicist is a person who has internalized two conceptual goals:
(a)The intuition that all of existence is an object available for contemplation to the human mind.
(b)This existence is knowable through reason and is deeply constrained and/or regulated by rational laws, laws that can be discovered by the process of mathematical thinking and experimentation — though a hard core theoretical physicist would dispense with the experimentation part and say that all of existence is fully determined by a certain set of rational principles.

Indeed, this also explains why physicists have replaced sages and mystics in our secular pantheon of realized beings — for they do represent the profoundest modern effort to capture all of existence in one unified scheme. I would go further and say that contemplatively gifted young people go into mathematics and physics because it is their best source for opening up to religious impulses in a culturally respectable way. We can explore how to open up this ontological, objective conception of Being, but for the moment notice that this conception is riddled with paradox and contradiction, related to the role of the observer who knows Being.
(a)Is this observer just another object among others (which is the normal picture), in which case a part of Being conceiving all of Being. If the observer is finite and Being is infinite, then it is really puzzling as to how the finite can conceive the infinite. If both the observer and Being are finite (as most modern science assumes) then we are truly left with an incredibly reduced conception of Being from which there may be no escape.
(b)The observer is not part of this objective conception of Being — a hypothesis that crops up repeatedly in discussions of subjectivity and consciousness (including Descartes’, who excluded the human soul from his catalog of machines). If indeed this is the case, then our conception of Being is limited, since it does not include the observer, and somehow the notion of an incomplete Being just seems unsatisfactory.