Avraham enters into a covenant with Hashem, that his descendants will be many, they will be great, and they will inherit the land. The sign of the covenant, is circumcision, the bris milah.
At the beginning of the parsha of milah, the pasuk says:
וַיֵּרָא יְהוָה אֶל-אַבְרָם, וַיֹּאמֶר אֵלָיו אֲנִי-אֵל שַׁדַּי–הִתְהַלֵּךְ לְפָנַי, וֶהְיֵה תָמִים – And Hashem appeared to Avraham, and said to him; “I am The Omnipotent, be before me, and be perfect”. (17:1)
The Beis HaLevi explains that people who deny fundamental precepts of Judaism, or even Hashem, can sarcastically ask that “if God can do everything, why do we have to do anything? Let Him have made the world perfect!”. They feel that the existence of imperfection disproves God. In the context of milah, the question is the same, that “if God wanted you circumcised, why didn’t He make you that way?”.
The Beis HaLevi points out that the name Hashem appears to Avraham with is אֵל שַׁדַּי. Chazal teach that this means the Omnipotent, that Hashem could have kept creating and building from Creation, but said דַּי – “enough”. Had Hashem not chosen to stop, creation would manifest itself perfectly, where all living things would give birth to adult offspring, food would not need processing or cooking, etc.
But Hashem said “enough”. Creation is not meant for us to enjoy in perfection, as the Torah tells us at the onset of Shabbos, the transition from Creation to existence, כִּי בוֹ שָׁבַת מִכָּל-מְלַאכְתּוֹ, אֲשֶׁר-בָּרָא אֱלֹהִים לַעֲשׂוֹת – for on that day did Hashem refrain from all His work, which He made to be done. (2:3). The point of existence is לַעֲשׂוֹת – to be done by man. Our instruction of וֶהְיֵה תָמִים, to be perfect, is our own responsibility.
Circumcision, and everything else in life, do not come naturally. They require input of effort and hard work, but it is the end goal of being here – to be perfect.