I think the overarching statement that this powerful novel makes about humanity is the way in which the novel constantly shows that the boundary between what is classified as "good" and what is "bad" is blurred. It is very difficult to determine what action is "good," as even those actions that are done for the good of humanity, like, for example, the training of Ender, is very bad, as is made perfectly clear by the way that Ender is mistreated, isolated from those that love him and placed into dangerous situations without any support or defence. Consider the conversation that Graff has in the final chapter where these crimes are explored in further detail:
People were crazy for a while there. Mistreatment of children, negligent homicide--those videos of Bonzo's and Stilson's deaths were pretty gruesome. To watch one child do that to another.
Such hideous crimes are justified, in the end, as Graff says by what was "necessary for the preservation of the human race," yet one of the biggest questions that haunts us as we finish the novel is whether such activities and blatant mistreatment of children can ever be justified, no matter what the threat facing the human race is.
The biggest example of this however is Ender's destruction of an entire species. He is lied to throughout, thinking that it is just a game, whereas in fact he is committing genocide to an extent that is unimaginable. The way that he is tricked into being a murderer is again representative of the blurred boundaries between good and evil. He saves humanity but only by being deceived into slaughtering an entire species, and this is something that haunts him for the rest of his life. The message of the novel seems to be that the two concepts of "good" and "bad" never exist by themselves. They are always muddied or tainted, as good slips into bad and vice versa.