"Performance" at all costs isn't what a manufacturer wants.  They want the best, most efficient performance that will still provide the engine a very long lifetime and keep the cost down as much as possible

Some things an aftermarket filter might change:

* More expensive
* Requires more maintenance (like an "oiled" K&N Filter)
* Could increase engine noise
* For a filter that deletes the air box, you have a higher chance of sucking in water or dirt, and even more sound increase
* I guess increased air flow could change fuel economy (guessing for sure)

What is an air filter for?  

To provide clean air to the engine of course.  The air box (filter housing) on most cars also provide some safeguards for sucking in water in the form of large splashes from puddles, but the filters only real job is to keep small particles out of the engine, and to not restrict the air flow too much while doing it.