Intake helps, get more air into the air filter cover box, or get a cone filter for your bike motor. Exhaust helps too, but intake matters more.
2 examples:
Just removing the air filter box cover to get open air into the stock air filter on my bike-trailer 196cc 4-stroke made a VERY noticeable difference in acceleration and torque, and much better sound under load. It also helped the engine rev better in the high RPM. Exhaust still stock.
I had a 2001 Ford Ranger with a high-revving Duratec 16V I-4 engine, and after making a huge 6" x 3" breathing-vent in the airbox in place of the stock 2 inch hole for the air to enter, the difference was amazing! Engine was much louder under load, revved to 6000RPM limit MUCH quicker. That was with a STOCK air filter too! Adding a K&N made it even better, but the most difference is getting the air to flow better in the first place. BTW, exhaust still stock.
2 strokes may be a bit different, but I highly recommend opening the intake flow on any engine to get better power. Always worked for me, and costs nothing to modify an airbox to flow better. Don't worry so much about the air filter, the air has to get to it first.