In theory a 2-2 system will produce better power at the top end of the rev range due to it's larger effective overall tube diameter, whilst a 2-1 will favour power at the lower end or the rev range as the effective diameter is smaller.
It is a good deal more complicated than this though. It is all to do with exhaust gas velocity (EGV) and exhaust gas flow (EGF), or rather the balance between the two. Essentially a narrow diameter pipe (2-1) will increase EGV and skew the torque curve towards the lower end of the rev range, a wider pipe will skew things towards the upper end.
Ideally you want an exhaust system where gases exit the combustion chamber and speed along at the highest velocity possible - you want a FAST exhaust stream. While it is true that the narrower the pipe, the higher the velocity of the exiting gases, you also want make sure the pipe is wide enough so that there is as little backpressure as possible while maintaining good exhaust gas velocity. The trick is to have a pipe that that is as narrow as possible while having as close to zero backpressure as possible at the RPM range you want your power band to be located at.
A perfectly tuned exhaust system will have high velocity, and will create a negative pressure area in the exhaust port exactly as the exhaust valve is opening. This makes the high exhaust velocity pull (scavenge) the gases out of the cylinder. Otherwise (if the exhaust is too wide and free-flowing) the piston needs to PUSH the exhaust out, as well as get the static/slow moving gases in the pipes moving as well which creates high pumping losses and robs power.
Now on single cylinder engines running at relatively low rpm, exhaust design isn't all that crucial and the differences minimal. Much less so than on multi-cylinder bikes where the power pulses from different cylinders can be tuned to help scavenge the combustion chambers during valve overlap (or hinder scavenging if the exhaust is designed badly). Now on a parallel twin for example, the differences between a 2-2 and 2-1 system will be significant, but on a single it's all a bit academic. A single will run perfectly happily with a single exhaust port and header (or a suitable diameter) - take the KTM 690, that makes plenty of power with a 1-1 system.
You may well find more power with a 2-2 system, but that is just mathematical power more often than not. Due to the fact the peak torque, although in might be the same as with a 2-1, it will move upwards in the rev range and because of the way horsepower is calculated from torque (torque x rpm/5252), means that on paper the engine produces more power. Remember a dyno can only read torque, horsepower isn't measureable in itself. Basically 1lb/ft of torque is worth more in terms of calculated horsepower at 7000rpm than it is at 6000rpm. However, the slower EGV in a 2-2 may well make the engine feel less tractable and torquey than with a 2-1.
Whatever you choose, the differences will be minimal and as previously mentioned, things like styling, weight saving and ground clearance are probably more important factors to consider. Just go for the one you like the best!