During embryological development, while the heart is still being formed, there are a number of unique features..
1. There a direct communication between the right and left atrium (foramen ovale). This allows placental oxygenated blood to directly enter the left side and then to the rest of the body.
2. During development, there is no barriers between the atria and ventricles. Rather, the communication between the two chambers is called the atrioventricular canal, and the walls of these canals are called the endocardial cushions.
3. It is thought that as blood flows from the right atria to the left atria, the central endocardial cushion bulges toward the left as well.
In so many words, this asymmetry and bulging causes fusion of what have been 3 cusps into 2 cusps on the left side. Whereas on the right side, the absence of an endocardial bulge allows all the cusps to separate independently.
I don't know if this is the only hypothesis, but check out the link, it provides a better explanation than I did above.
Hope this helps!