Truly, there is divine wisdom for every act of worship prescribed by Almighty Allah or by His Prophet (peace and blessings be upon him), but we cannot know the wisdom of every act, so we have to worship Almighty Allah and practice the act whether or not we know the wisdom behind it.

Mufti Muhammad Taqi Usmani, deputy chairman of the Jeddah-based Islamic Fiqh Academy of the Organization of Islamic Conference, stated: Forms of worship are prescribed by Allah Almighty and have been conveyed to us through the Prophet (peace and blessings be upon him). No doubt, every form or method of worship is prescribed with some wisdom behind it. However, that wisdom has not been expressly mentioned in the Noble Qur’an and Sunnah in every case. We can attribute certain reasons for certain acts, but it would be a hypothetical exercise that may or may not be correct, because the real wisdom is best known to Allah Alone. The number of rak`ahs in the Fajr Prayer is two while it is four in Zhuhr Prayer, `Asr Prayer and `Isha’ Prayer and three in Maghrib Prayer.
the reason for the different numbers of different Payers is not mentioned in the Sources of Islamic teachings. The way of praying also varies. We are directed to recite the Qur’anic verses while standing in the Prayer, but we have been forbidden from doing so in the states of ruku` and prostration. Likewise, Tashahhud has been prescribed in the state of sitting and not in the ruku` or prostration. The exact reasons for these directions are not expressly mentioned in the Qur’an or in the Sunnah, because the essence of worship is nothing but to obey the divine commands and to follow the prophetic practices even if their reasons are unknown.
Similar is the case of the du`aa’Al-Qunut. It has been prescribed in the last rak`ah Witr Prayer without giving any reason. Therefore, we must follow it even though its exact reason is not known to us.
One can say that since the Witr Prayer is the last prayer performed by a Muslim at night, a comprehensive du`aa’  has been prescribed in its last rak`ah so that one’s daily activities may end with this prayer which encompasses all his needs, both in this world and in the Hereafter.
However, as mentioned earlier, this is only a possible reason. Another person may adduce other reasons, while the real wisdom is known only to Almighty Allah.