Can Air Filters and Exhaust Pipes Really Increase Motorcycle's Performance?

To understand that question, we need to understand what is breathing. 

"Breathing (or respiration, or ventilation) is the process of moving air into and out of the lungs to facilitate gas exchange, mostly by bringing in oxygen and flushing out carbon dioxide." -wiki

Now we have that cleared, we often confuse how an engine breathes to how we breathe.

                       We take in air through our nose, lungs absorb it and the nose expels the CO2 gases.

Not How Engine Breathes!

This is not how the Engine Breathes. The engine needs oxygen to combust and convert to energy.

But it does not have a single inlet and outlet path (nose) for moving the air.

To better understand the engine, a diagram of Jet Engine, which is also a type of engine can be used. It is very similar to IC engine but just laid out in one stretch.

The Three Stages: Intake, Compression - Combustion, Exhaust

Air Filter takes in the air.

Which is Compressed at the Combustion Chamber and then combusted along with the fuel

The fumes are then expelled through the Exhaust

Now Imagine if we Increase Just One Stage,

Increase Intake by adding some Free Flow filter - Combustion will have a problem because more air is going to be pushed in than the engine needs. 

Irrespective of whether it was carburated or fuel injected, it would still have higher intake pressure causing almost impossible to attain low-end throttle.

Even a small increase in throttle will result in higher RPM rise, perceived as a power increase by Road Side Rossis, but is not increase in power but skipping of low RPM ranges.

Increasing the fuel intake by re-jetting the carburetor or adding a fuel commander (more info on that on another day) will increase the fresh air requirement from the filter, which it can not procure. And exhaust pressure

will be created, however, the exhaust is not designed to push SOO much air out. So it will create a back pressure that will cause malfunctioning of the valve timings.

End Result: Not Good for the Engine

Adding a Shiny New Exhaust, and increase the final stage alone is one of the most commonly done cosmetic and acoustic upgrade done.  This will make the exhaust a free flow and it will want more air from the engine; which it can not provide hence again causing malfunctioning of the valve timings. Hence the same end result as above.

Because of the above inferences, it is never advisable to upgrade only one stage for any engine. 

• As a side effect of upgrading air filter or ECU remap can all be felt as increased performance in the short term. But on the long, it affects the life of an engine.
• Air Filters or Exhausts claiming to increase bhp are all just stickers.
• To actually make a good increase in performance we need to upgrade to free flow air filter, remapped fuel mapping and free flow exhausts - all at once.

And still, 

           the question of whether the engine was initially factory designed to produce higher power is skeptical to answer - read on at OneHTW - Engine Life to understand why RnD is to be respected.

And is it really worth to increase performance more than stock - is yours to answer...