spyder,
When it's iffy what the home-owner may want, I have been known to do as you said with switched receptacles and run 12-3.
On bid jobs with plans, they get exactly what's on the plan. Anything else is a change order. Period. (I'm getting tougher in my "old age"). Then, of course, it's simpler to run a switch loop if only one location is to be switched.
As always, I take each and every situation and weigh the pros and cons of each method.
Usually, but not always, I run the neutral through the switchbox.
