It can be useful to look at things, when comparing, as sets of similarities and differences. This is a sort of general proposition--into which I'm undoubtedly going to stick some things that are unlike.
Recently I struck up an acquaintance with a professor at Cal who happened to ask me an editorial question one day as we were working at adjacent tables in a cafe. We got to talking and he was discussing his attempts to teach his students to write. On the one hand, we both agreed that it was a great exercise to attempt to write a one-page synopsis of the entire work, on the other, his focus was more on the outward form of the writing, while mine was more on the inner motivation for the writing. Similarities can give rise to greater conviction: we both agree that a specific tool is useful. Differences can give rise to options: our differences in focus present us with different ways of looking at a project, which can give us a choice of options.
When we're working with other authors, it can be helpful to keep in mind that there will typically be areas of agreement and disagreement. When we're working with whole fields of study and their discourse, we're even more certain to see areas of agreement and disagreement. By being aware of both the similarities and differences, we can use comparisons with others (especially with those who are well-known) to help our readers see what our theoretical position is and where it fits into a larger discourse.
A good friend of mine ran into problems on his qualifying exam because he was unwilling (or unable) to choose between using similarities and not differences. My friend, who was philosophically a Pragmatist in the tradition of James, Pierce, and Dewey, did not like the work of Donald Schon. I cannot remember his precise objection--I think at one point Schon had written about use of rules, and my friend didn't like the idea of rules, and so would vehemently object to Schon in general. On his qualifying exam committee, however, sat a professor (or two) partial to Schon's work. The Schon issue became a point of contention, to the extent that he was passed on his exam only with the condition that he write an additional paper about Schon.
What surprised me about this was that Schon and the Pragmatists are not unlike. They both are writing from a point of rejecting the pure rationality suggested by a Bertrand Russell, for example, or by the supporters of Operations Research. To the Pragmatists, as I understand it, truth is "what works"--it is fluid, and dependent on the observer/experiencer. Schon, too, held that the vision of a problem was largely dependent on personal experience. Both rejected the notion of some external absolute and objective truth. To me, then, I see an opportunity in the comparison to note both similarities and differences. And a choice of which to focus on.
In the case of my friend, there were some other relevant similarities and differences. He, like the member of his committee who supported Schon, would have rejected standard rationalist paradigms of understanding as good models for behavior. That was a similarity. And unlike the committee member, he disliked the work of Schon. That was a difference. By choosing to focus on the point where Schon and the Pragmatists disagreed, he also choose to focus on the point where he and his committee member disagreed.
I'm not suggesting that one blindly say whatever your professor thinks is right. That's a lousy way to live, and not really a good way to impress a professor, either. But by using a comparison that looked at both similarities and differences, I postulate that my friend could have saved himself from the extra paper. If he had been able to highlight the similarities, and give them attention matching the attention he gave to the differences, I suspect his reception would have been different. Acknowledging the similarities would work on a personal level to build a bond of agreement; that would work in his favor when it was time to talk about the differences. Acknowledging the similarities would also show a theoretical sensitivity that might work in his favor: by failing to acknowledge an apparent similarity, it might lead a listener to believe that he was not fully aware of aspects of the theory, or that he did not understand the theory. By using both similarities and differences, we can appear perceptive and able to handle subtle nuances.
This matter of similarity and difference can also come up in our writing. As we write, we should have a general sense of where we want to go. Then, as a we work, we want to bring in the material we have that furthers our sense of direction. But evidence and ideas are varied and complex, and getting an argument that is without problem is more than we can hope for. Instead, we look to manage the material: we build a strong central core around those things that work best together and have the greatest similarities, and then around the edges of our argument we place all the problematic stuff--the places of difference--and manage those so that our argument, when constructed, works with a main body of evidence, and then acknowledges the problems, limitations and unanswered questions that our main argument has created.
We want to build around the places where our ideas and evidence best cohere, and then work with the places that they come apart. We don't want to let our attempt to build a coherent story out of similarities close our minds to the possibilities that our basic hypotheses are wrong: we don't want our sense of purpose to destroy the intention of objectivity and open-mindedness. But at the same time, we cannot let the fringe problems destroy the central argument. Arguments tend to be problematic--certainly there is good reason to believe that arguments will never attain the sort of logical purity that Descartes sought (and claimed to have found): from those who observe the presence of paradox in logic (e.g., Kurt Goedel and his proof of the incompleteness of arithmetic, or the many paradox described by Borges in his essay "Avatars of the Tortoise"), to those who argue that all logic, knowledge, etc., is ultimately founded on social issues (e.g., Whorf and the Whorf-Sapir hypothesis, or Foucault), there are plenty of reasons to believe that our arguments will, at best, have some weaknesses to deal with.
By being open to focusing on the similarities and/or the differences, as suits our immediate purpose, we can, in the long run, develop an argument that coheres to the extent it will cohere, and acknowledges its weaknesses in an appropriate fashion--and in so doing, we will be following the best precepts of philosophy and research.