One of the other factors include air/fuel mixtures. Most stock motorcycles run lean at part throttle to meet emission regulations. This leannes inhibits roll-on performance; how-ever, it is simple to correct. A simple needle change and re-tune of the stock carburetor or slight re-tune of an EFI system are required to correct the emission-related air/fuel mixture problem.
Beware, a number of aftermarket kits are available for the stock carburetor that mostly claim your money. Some of them reduce mileage substantially and get so rich with altitude that the engine may misfire. Some also begin to wear and perform even more poorly within a few thousand kilometers. You only need to change one part in your stock carburetor to correct the lean mixture problem; use carburettor needles from a source you can trust.
High-flow air cleaners/air-filters are not as important as you might think. While the single greatest peak power gain comes from fitting a high-flow air cleaner/air-filter to an otherwise stock engine, that power gain does not begin until about 6,000 rpm and nets only a couple of horsepower at that revving level. All it will do is make more noise at lower rpm's and might drip oil/sweat out of the exhaust-pipe.
Most of the time the stock filter assembly does well in the range we are concerned with for gaining more torque.
As for exhaust systems, in general, the louder they are the less good they do in the mid-range. In fact, most of the power you may think you feel you're getting from aftermarket mufflers comes from the psychological effect of the added noise.
The easiest, cheapest and most effective way to truly improve acceleration is to simply downshift. That's right, downshift. In a fraction of a second you can greatly increase power to the ground. If you downshift twice, you might even double it.