RPM + Aero doesn't quite level the playing field, but does count for a lot. As well as the fact it fires on every revolution.
As for the 18-20,000 rpm 4 strokes, an equal displacement 2 stroke would **** all over it. And when you divide 20,000 by 4 you get 5000. So the equal displacement 2 stroke firing 5000 times a minute would be roughly equivalent to the 4 stroke at 20,000 rpm. And the 2 stroke wouldn't be near redline either. (I could easily be wrong).
4-strokes however, offer a lot more when it comes to aftermarket modifications.
The bottom line is, that there is a lot to be said for the 49cc engines, and It's annoying when people knock on them without experience.