Good read, both of them. My thoughts on intake systems are basically the same as what Mishimoto tells about in both parts of the article. Ultimately, it comes down to the specific vehicle, application, and what kind of intake you are using. They won't blow you out of the water in terms of gains, but when done right, can give you a bit more power. The manufacturer doesn't install them from the factory because they have budget, sound, and repairability/maintinence constraints. If they sacrifice 2% power to meet an intake noise requirement, chances are they will take it.
For most part the Factory Air Boxes and Systems are going to give optimum all around Air Flow for that Vehicle. Too many blow and waste money on 3rd Party CAI's and in most cases it only makes the more prevelant Noises of Air Sucked in and Pumped out of the Exhaust but does not necessarly give you optimum HP and Torque if any, in some cases you loose HP because they suck in more Hot Air from under the Hood by being Open Systems. Even if more Air goes in if its Hotter Air you will loose HP its a fact.