There are a few principle differences in these historical tragedies. For one, the T-4 program was directed at a different population - the mentally disabled, as opposed to the Jews, Gypsies, Homosexuals and Communists targeted by the Holocaust. Hitler had no intense personal hatred of the handicapped as he did with the Jews, it merely fit with his vision of racial purity to kill them.
Another key difference in this program is that the German public resisted the T-4 program openly. Clergymen, doctors, civic leaders - many spoke against the program almost fearlessly, leading Hitler to eventually shut the program down. It's also important to note that T-4 was not run by the SS, as the Final Solution was.