The stock intake draws from inside the fender to get fresher air than if it was open to the engine compartment. The intake is somewhat protected there. When fording water, the wave will curl down about where the intake is so that the front of the wave isn't sucked in. That air is also, somewhat, cooler since it is outside the rig.
Yeah! I agree. I've posted about this before a few times but a K&N or similar drop-in high-flow air filter is the best bang-for-buck and performance-for-effort -- literally a one-minute mod and keeping the factory set-up intact makes for zero guesswork.