A major issue to consider in doing systematically consistent apologetics would be to examine the implicit theories which underly your apologetic answers.
The First Three Flat Irons, Boulder, CO
Photo Credit: JAC
That wouldn’t seem to be much of a problem since you’d expect a theist to think through her world view (and thus her apologetics) as a metaphysical theist. That is, you’d expect her as a Christian theist to be a theistic realist and you’d also expect her to think through how such a position would or might play out on the realist/irrealist divide in science (where the irrealist position is typically called instrumentalism), play out in moral theory, play out in the mind/body problem and so forth.
Now it is true that theists may have more than one legtimate option concerning how this could play out in specific cases like the mind/body problem, but surely she should begin thinking about the problem bringing her metaphysics about God. Not uncontroversial, but as a first approximation you’d also think that the “thicker” ethical information that the Bible provides might inform her as she looks for ways this could play out as she addresses other relevant issues. However, a word of caution seems appropriate.
First, important as metaphysics is, an explicit systematic exposition of what makes for a Christian perspective of metaphysics is not part of what has historically been included in the great doctrinal creeds of the Christian faith; and, much of what would be considered systematic exposition (for instance, as by Augustine or Aquinas) is not a part of what has been considered explicitly orthodox or heterodox. It’s true that historically Christians seem to have taken a mostly one sided view on some specific metaphysical cases like a “theistic realism” about God’s existence, or on taking a "multiple substances" stance on the mind/body problem. However, there are more than one metaphysical position that have taken by orthodox Christians regarding even the existence of an external world—cf. Bishop Berekley’s idealism.
Another factor to consider is the history of theology and philosophy that teaches us that theologians and apologists have borrowed ideas and concepts from the metaphysics of people like Plato, Aristotle and their followers, as a means to think through and explain important issues in theology. However, it should be noticed that Plato and Aristotle and their followers don’t happen to agree with each other on important issues; and thus, subtle but determinative conflicts can come into play. Therefore, one has to be heads up on the metaphsical schemes one brings to theology.
Third, and this is closely related to the word of caution just above, having to do with working out one’s theology with our metaphysics. Since metaphysics can precede in many ways our interpretation of what is being said it can go unnoticed in the analysis. For instance, we might take for granted in our interpreting of scripture that there’s a distinction to be made between what we call mental properties and physical properties in scripture. But, the question is what did the original authors mean to say and are we possibly bringing in our metaphysical understanding and reading it into what we think is most likely what they meant to say. This can be complicated because there is the question as to whether the authors of scripture used language to accommodate their hearers and were not using it precisely to illuminate doctrine. Well, it seems a case can be made for sometimes they seem to be doing that (using their language precisely) and other times they seem to be accomodating what they say to their audiences. It’s case by case. Thus, with caution we want to check our theologies and research projects for these sorts of possible oversights.
In Deconstructive Apologetics:
Remember, too, apologetics involves not only defending theistic beliefs in a consistent 
way, but also questioning beliefs held by non-theists. That’s what we have called from the beginning “deconstructive apologetics.” This will be covered in greater detail in later apologetic levels on this site, but we wish to comment on it because it does have some relevancy here.
One major part using metaphysical consistency as a tool in one’s apologetic toolbox is to examine whether or not those who hold opposing views, like metaphysical physicalists or materialists can give coherent explanations. For example, do they have a sufficient basis for claiming the brain can do what she might claims it does. That is, can the brain and/or the properties of the brain construed entirely in either materialist or physicalist terms adequately account for libertarian freedom, which by the way is needed for ethical and even rational responsibility? If she can’t, the alternatives, strong determinism and even soft determinism (compatibilism), which seem to comport with materialism and physicalism are very problematic. Those weaknesses, which we will discuss elsewhere, can be properly exploited by an apologist who wishes to show the inadequacies of a competing system of thought.