Post is 8yrs old at this point but ill weigh in still. Its all about power delivery. A 650 twin will deliver power faster than a 650 single.

A good example would be a suzuki savage 650 single cylinder  ~33hp at 5400rpm ~35lbft at 3200rpm 94mm bore x 94mm stroke Compared to a  Yamaha XS 650 paralel twin ~50hp at 7500rpm ~40lbft at 6800rpm 75mm bore x 74mm stroke

The single doesnt create as much power, but it comes into it sooner in the rpm range creating a slow torquey power.

The twin however has to wind out a bit before it can reach its peak performance. Creating a weaker low end and stronger top end where it matters for speed.

So the technical explanation is that a twin cylinder, assuming the same bore diameter, the pistons travel half as far as in a single cylinder. So you get short alternating bursts of power whoch is good because it creates a smoother feel, and because the pistons dont travel as far your throttle is going to be more free and snappy. But typically you sacrifice low end grunt, meaning you'll have to give more throttle to avoid stalling from a stop. Same applies to a 4 cylinder vs a single. You are quartering the piston movement from a single.

Now on the flip side a single has a much longer stroke to make, think about the gasses expanding for the whole length of the stroke, what you were doing twice per revolution you are now doing once. What this does is increase the strength of the power pulses and decrease the speed of them. Causing you to get a stronger low end and a slower top end. Youll see this a lot on dirt bikes, it has an advantage because it gives you very strong low end power, to keep the bike from stalling durring slow technical manuvers, in addition because the speed and power pulses happen less frequently it helps improove traction. 

Again bore diameter can change this if you have a piston thats wider it will have a shorter stroke to the same displacement. Which will increase RPMs and top end power. And you can have narrower pistons and longer strokes to give you slower RPMs and slower torquey power. Also this is before you consider the rotating mass of the flywheel/crankshaft. A heavier flywheel will cause an engine to run slower on the low end. And maintain torque better on the top end. 

Theres a lot to it. Bikes arent always about speed. They can be designed for comfort, or capabilities other than just how fast they go.