Recently I published an analysis of the extent to which the ecological literature engages with theory (http://onlinelibrary.wiley.com/doi/10.1111/ele.12196/abstract). One part of that analysis was a comparison of current journals. Among the ecology journals, Oikos scored the highest with 73% of the papers in the 2012 June and July issues including some aspect of theory development or testing. But we can all do better. Here are some ways to increase the theory engagement of your papers.
First ask yourself, “What theory does my paper relate to?” Even if your paper is a description of some system, that description must relate to the facts that underpin some theory. Theories rely on generalizations. Does this particular instance help strengthen a generalization? Does it dispute a generalization? Is the state of knowledge such that generalizations are uncertain? If so, how does this paper reduce that uncertainty? Then make that theory and those generalizations guideposts for the entire paper.
But you say, “There is no formal theory for this question, just a general understanding.” That general understanding is the theory, it simply lacks formalization. In the parlance of the theory structure presented by Mike Willig and myself, no constitutive theory exists. Here is an opportunity for you to create one. Formalizing a constitutive theory is not difficult. For examples of how to do this, see our book (Scheiner and Willig. 2011. The Theory of Ecology. University of Chicago Press). If there are already numerous models relating to the topic, it is an exercise in finding their common threads. That is the process that we went through with our first constitutive theory (Scheiner and Willig. 2005. Am. Nat. 166:458-469). For more nascent fields, you may have to work a bit harder to discern those threads. In the end you will have a list of rules and generalization (“propositions” in our terminology) against which to compare your data.
As a reviewer of papers, ask if a paper engages in theory right at the beginning. My tally of “no theory” papers included many for which formal theories exist, but no explicit connection was made. Make sure that this happens. If the introduction of the paper does not explicitly name a theory, insist that it do so. We should be asking more of ourselves. Ecology is a mature discipline rich in theories. Our science will only be strengthened by all of us doing more to engage with theory and insisting that our colleagues do likewise.