I know you were trying to do a basic outline, but there are a few important facts about intake and exhaust systems that are missing.
Intakes:
Short ram intakes can cause a heat soak issue when you are moving from a stop, although I feel this is often exaggerated it can be an issue. However, you will not see this problem on dyno charts as the car is usually sitting there with the hood open and fans blowing onto the intake.
Cold air intakes are more prone to a hydrolock situation, where water may be sucked into the engine, and can cause problems as water does not compress like air does. I have noticed some people having problems with the filter getting wet in heavy rain and the car not running well or stalling out.
There are several types of aftermarket replacement filters available, and you must be careful when choosing one. The K&N filter comes to mind. Although a great marketing success, many people still question how well it actually filters out particulates in the air. There is also the problem of getting the right amount of oil on the filter.
One thing of note on stock intakes is that depending on your car the stock system may actually be much better than the current after market systems. The current generation Civic Si (FG2 and FA5) has a cold air intake system on it from the factory. This system is not prone to hydrolock, and some may argue that the plastic intake design may actually be less prone to heat soak than a metal intake pipe. However I have not seen any evidence to prove that so at this point I believe it is just conjecture.
Here is Honda's diagram of the k20z3 motor with the intake shown on the right.
It is also worth noting the level of complexity of the above stock intake. I have not yet seen, other than the incredible expensive Mugen intake, an intake system on the FG2 or FA5 that is capable of increasing power across the rev band, almost always they show a drop of power in the lower revs, which is an area where our smaller displacement cars need power, and the part of the rev band you will be in most often for daily driving.
It is definitely worth pointing out that on the FG2/FA5 it has been noticed that using a throttle body spacer and performing a throttle body coolant bypass has provided essentially the same increase in HP (about 10hp) as using a CAI according to the dyno.
On exhaust one thing worth noting is that many headers that are sold for our cars are "race headers" which remove the cat. Although this does free up a lot of restrictions, it is illegal, really can make your car smell like a junker, and is immoral for reasons of pollution. I agree with your view of leaving the cat in there.
One thing of note is that it has been proven on the dyno that headers such as Comptech's shorty headers do increase top end horsepower, but at the same time sacrifice a bit of low end torque.
Its not a bad article, and I probably went more in depth than what you were looking for, but I think that people often overlook the level of work Honda's engineers do in order to maintain both peak horsepower and decent torque for daily drivability.