An after-market exhaust is usually intended for a rider who wants greater performance, which means greater acceleration. They expect to have to rev the engine in the upper range to get that extra performance. It's to be expected that the factory exhaust imparts greater low-RPM torque compared to most after-market systems.
An exhaust system can not increase power at all RPM, especially without additional engine modification. A system designed for high-RPM acceleration can not perform well at low RPM, and vice versa. The greater the performance boost, the narrower the RPM range of that boost, at the cost of performance outside that "power band".