I think of this as a subjective thought based on theory which often leads our thinking as acupuncturists and we have plenty of sources expousing theory. Underneath it is the objective analysis ... did it work? Ultimately, what is most important to me is what works. And intention, I believe, from our thoughts carry through to our patients.
I was born in Missouri which is known as the Show Me state. So they did this study with doctors and prayer for those that were sick. The had people who did not even know the patients pray over them with a control group with no prayers. The "prayed over group" got better at a higher percentage than the control group. It has been my observation that the intention of the practitioner has a bearing on results.
In terms of theory, I use it to direct my intentions. So often I use the male or female sides first when approaching a male or female. For me, I get better results. It is only one of many ideas. If you needle on the opposite sides for a paired point solution, then that is referred to as spinning the point. The directed energy catches up to the energy cycling through all 12 meridians and when it does it increases its velocity or puts a spin on it. So I find this applies all over the place. I find it increases the effectiveness of treatment and one uses 1/2 of the needles.
I use it on Li 4 and Lv 3 (or 2 with heat). I use it on back shu transporter points. And have found others that do the same that have many more years experience than I do and they find it improves their treatments. Alex Tiberi in his clinic halved his back shu treatments and told me that it was more effective for him.
I also listen to the pulse and look to the tongue to guide this analysis. If one side is wiry and the other side is choppy, I may treat a spin on one side to rectify Qi (Li 4 and Lv 3/2) and a spin on the other side to invigorate and cool the blood while boosting the immune response (Li 11 and Sp 10). I like to treat and re-check the pulse and verify the difference.
As these theories conflict, follow what makes most sense and what brings best results. You will not know unless you are looking and trying new things. One of my favorite reads has been the art of a single needle point. Not because a single needle is all you need but because it took a finer look at the details of the patient to narrow the field down to a single needle.
Many other parts of the body give clues. Akabani (incense heat readings at jing well points) tells the balance between each meridian and if the feet are high values and the hands are low values -- you have a belt block problem and need to open the dai mai channel. Once again I would spin this with SJ 5 and GB 41.
Now which side to choose from this problem? It depends on what other problems are there and what feels dominant for that person. It wraps back to your intention to help by treating what you see. I like to think that I treat what I see. The more clearly we see it, the more effective the treatment.
The beauty of this system is that each of these check points also show whether the body is improving. Another testament of the pragmatism of this line of reasoning.
What is best in acupuncture? Diagnosis, Diagnosis, and Diagnosis. Because you can look back and understand why you tried what you did and see if it worked or not. At least for me if my intention wanes then my practice suffers.