There are soooo many reasons your airbox could be coughing... e.g. mine's coughing at the moment but it's carb issues (nothing to do with the airbox), so Factory Pro Jet Kit is on it's way to me. Other guys here have coughing airboxes because their inlet valves are shot...
But to answer (or not) your question. Lot's of research indicates that the aftermarket 'standard' filters don't let much more air through than the stock. Having said that, if you're planning on opening your airbox up, some aftermarket filters filters are more durable and less susceptible to damage from moisture etc.