I always look at it on how often you are willing to clean your computer...
If you run 2 intake you must clean more often as the amount of dust and other nice stuff entering the system is greater. The flip side is the more cool air entering gives a positive reaction for cooling...
In my systems I do a 2/1 method, because I know people do not clean their systems as often as they should. 1 in 2 out, in the case of my personal computer I have 2 in the front, and 1 in the base are all intake, with 2 in the center (interior flow fans), then I have 2 rear, 3 top. Now the 2 center fans I do not count in the equation as they just move air from 1 point to the other.
You just have to ask yourself how much are you willing to break down your comp and clean it. With my setup I do a thorough cleaning once a month. That is a complete tear-down.