Just like with any other internal combustion engine, there are two ways to increase power output: add more cubic inches of displacement; make the motor think it has a larger displacement.
The rotary engine (Wankel) is a different breed. You cannot just bore/stroke the engine like with other piston based engines, so you have to go a different route. The easiest way with these is to add more rotor lobes. There are kits you can purchase which will allow you to easily do this, though it does take some expertise. Each rotor of a Wankel engine should roughly be considered a 3-cylinder engine if it had pistons. By adding another rotor, you are making a 6-cylinder engine into a 9-cylinder engine (going from two to three rotors). This should have an effect of adding upwards of 50% more power to the engine combination.
Pseudo Larger Displacement
What I mean by this is to turbocharge your engine. When you turbocharge an engine, you are pushing more air/fuel into the engine, which can allow it to create more power. Due to the way the Wankel engine is designed, there are diminishing returns for this, though. Since there aren't any valves or camshafts, there is no way to control timing events to optimize how the engine will run with the turbo installed. Some of the air/fuel mixture ends up being burnt in the exhaust manifolds. This is a loss of power.
Other items in this same vane would be to look at other power adders, such as nitrous oxide, which throws a denser air/fuel mixture into the engine, causing more power to be created.
Mind you, this list is not all inclusive. As evidenced from the @cdunn and @racefever answers, there are other ways to increase power, just not as drastically as what I've talked about here.