Brian,
On some engines (bikes), the airbox cannot be made to fit and still have a good volume - the Rocket 3 comes to mind. Only in these cases will individual filters work better than stock.
The Rocket3 would be even better if the plenum (airbox) was designed correctly, but the 2.3L engine demands a BIG plenum volume.
There is a huge amount of info available on plenums and the Helmholtz pulse tuning effect. The days of open intakes without plenums are nearly past - for good reason.