I received an email from a nontheist that is somewhat critical of the idea of "naturalism vs. theism" as a debate topic because (1) not all non-naturalistic views are theistic, and (2) the topic involves a comparison of a general hypothesis (metaphysical naturalism) with an incompatible but very specific hypothesis (theism). In his opinion, the debate topic should be either "naturalism vs. supernaturalism" or "nontheism (or atheism) vs. theism."
I don't find these objections convincing in the least. (1) is, of course, true. From the fact that not all non-naturalistic views are theistic, however, it isn't clear why "naturalism vs. theism" debates should be avoided in favor of "naturalism vs. supernaturalism" or "atheism vs. theism" debates. A significant number of supernaturalists are theists. In the West, the majority of supernaturalists are theists. For that reason alone, I think "naturalism vs. theism" is a valuable topic. (I am well aware, of course, that there are parts of the world where traditional theism is not the dominant supernatural belief. That is no reason, however, for not having debates on "naturalism vs. theism" in parts of the world where traditional theism is the dominant supernatural belief.)
Moreover, I think there are additional points from a Bayesian perspective that make "naturalism vs. theism" as a debate topic particularly compelling. First, I won't attempt to defend this claim here, but I believe that theism has a much higher prior probability than supernatural alternatives to theism. Second, it is a commonplace in confirmation theory to measure the ratio of one explanatory hypothesis to another logically incompatible explanatory hypothesis, even if those two explanatory hypotheses are not jointly exhaustive. Again, even if the two explanatory hypotheses are not jointly exhaustive, demonstrating that the ratio of the probability of one hypothesis to the probability of another is greater than one can be used as part of a larger argument to show that the former hypothesis has a high final probability.
Turning to objection (2), it is true that naturalism is a general hypothesis whereas theism is a specific hypothesis. Again, however, it is not clear why (2) is supposed to be a reason for avoiding "naturalism vs. theism" debates in favor of "naturalism vs. supernaturalism" or "atheism vs. theism" debates. Outside of the philosophy of religion, we probably compare general hypotheses to specific hypotheses on a regular basis. It isn't obvious why we should avoid doing so, either in general or in the specific case of "naturalism vs. theism."