the ecu is set for stock parts ... when you add something like an intake and exhaust, you want the ecu to learn the proper air/fuel mixture. by resetting the ecu, you'll achieve the part's full performance. the ecu will learn the proper combo over time too.

for example

00 AV6 coupe + AEM intake + Comptech exhaust = 27mpg ... which is freakishly good for my car.