Perhaps the most important reason for the two-year home-country physical presence requirement arises from the purpose of the J-1 visa. The J-1 visa is not only designed to benefit you — it is also designed to benefit your home country.
Suppose, for example, that you undergo graduate medical training in the United States. One of the reasons that you were permitted to undergo this program in the first place is that your graduate medical training will benefit patients in your home country.
It would therefore defeat the purpose of the program to allow you to remain in the United States after the completion of your J-1 program, because in that case your skills would benefit US patients, not patients in your home country. Indeed, in many cases, your home country itself might object to your waiver application. A waiver is possible, however.