Hi BareNecessity,
Technically you're right, but a new air intake will give you better performance (due to increased airflow) and allow you better access to the engine. I put on a new air intake (aFe Magnum Force) and have been very pleased. I have noticed a definite increase in horsepower and torque - especially towing my little Scamp Trailer. Also, I have noticed an increase in MPG when on highway trips - about an extra mile per gallon. In the city, the MPG is pretty much the same. Also, you will never have to buy a new air filter - the filter that comes with it is guaranteed for like - just clean it and put it back on. Installation instructions were good and the job was easy to do.

Here is the link to the aFe site I ordered mine from. I purchased the one on top.
Toyota FJ Cruiser Air Intakes - Toyota FJ Cruiser SUV Accessories - AutoTruckToys.com

All in all, I think that it was well worth doing.
TommyBoy