The three main bottlenecks to producing big power from motorcycle engines are restrictive emission controls, airflow through the cylinder head, and the camshaft timing chains. Emission controls aren't an issue since most motorcycles already passed emission testing before thinking of more power and most of the emission related parts – air filter, carburetor jetting or fuel map, ignition timing, camshafts, and exhaust system – will be replaced with performance parts.
As for restrictive airflow through the cylinder head, at first glance, DOHC cylinder heads seem superior, and the are, in design but not in airflow. The DOHC design promotes a higher percentage of burn of the fuel/air mixture that's allowed in. However, these cylinder heads often do not let in the right fuel/air mixture for engine running at a lower rpm. For high revving engines, DOHC valves are the best choice, but for engines with a redline at say 8,000 rpm SOHC valves are probably the better choice. For mild high performance objectives – one with mild camshafts, the stock valve springs, a less-restricted exhaust system, and some intake system work, as well as an upgraded ignition – porting and polishing the stock cylinder-heads is the most economical way to go. Obviously, upgraded cylinder-heads will add more speed and power, but they also cost a good amount more.
Motorcycle dealers and motorcycle parts stores often overlook this obvious performance necessity and sell engine upgrades to consumers without informing them of this airflow bottleneck: the stock cylinder-head(s). Why would anyone increase the cubic displacement of an engine when you can't get enough air in to feed the stock size engine? Even if you're not increasing the engine's displacement, the first performance upgrade should be increasing airflow into and out of the combustion chamber.
I believe that the most motorcycle manufacturers did this to help create an good selling aftermarket. The design of the stock cylinder-heads is superior. If the factories increased the port and valve size on the stock cylinder-heads, there would be no need for many performance upgrades. Stock engines would flow more air, increasing the engine's breathing efficiency and fuel efficiency, with increased speed and performance as a welcome side-effect.