Wisdom behind Fajr prayer being two rak‘ahs

Firstly: 

Allah has enjoined upon His slaves five prayers to be offered each day and night, and He has prescribed the number of rak‘ahs in each prayer according to His wisdom and knowledge. 

So we have to accept, submit and obey, and to say as the Messenger and the believers said: “We hear, and we obey” [al-Baqarah 2:285]. For more information, please see the answer to question no. 65877 

Secondly: 

Al-Bukhaari (1090) and Muslim (685) narrated from ‘Aa’ishah, the wife of the Prophet (blessings and peace of Allah be upon him), that she said: Prayer was enjoined with two rak‘ahs in each prayer, whether one was staying at home or travelling. Then the prayer when travelling was confirmed (as being two rak‘ahs) and the prayer when not travelling was increased. 

Ibn Rajab (may Allah have mercy on him) said: When Allah, may He be exalted, enjoined upon His Messenger the five prayers each day and night, then he came back down to earth and Jibreel (peace be upon him) led him in prayer at the Ka‘bah, his prayer at that time was only two rak‘ahs in each prayer, whether one was staying at home or travelling. Then the prayer when travelling was confirmed as it was, and two rak‘ahs were added to the prayers when staying at home. What is meant here is the four-rak‘ah prayers only.

End quote from Fath al-Baari, by Ibn Rajab, 2/327 

Ibn Khuzaymah (305) and Ibn Hibbaan (2738) narrated that ‘Aa’ishah said: The prayers, whether travelling or staying at home were enjoined with two rak‘ahs each, then when the Messenger of Allah (blessings and peace of Allah be upon him) settled in Madinah, two rak‘ahs were added to the prayers when staying at home, but Fajr prayer was left as it was, because of the length of the recitation therein, and Maghrib prayer (was also left as it was), because it is the Witr of the day.

Classed as hasan by Shaykh Shu ‘ayb al-Arna’oot in his commentary on Saheeh Ibn Hibbaan. 

According to a report narrated by Ahmad (26338), the first thing to be enjoined upon the Messenger of Allah (blessings and peace of Allah be upon him) was prayer with two rak‘ahs each, except Maghrib, which was three rak‘ahs. Then Allah completed Zuhr, ‘Asr and ‘Isha’, making them four rak‘ahs when staying at home, and confirming the original obligation (of two rak‘ahs) when travelling.

Classed as hasan by the commentators on al-Musnad. 

This hadith explains that when the prayer was first enjoined, it was two rak‘ahs in each prayer, then that was confirmed in the case of travel, but it was increased when staying at home. So Zuhr, ‘Asr and ‘Isha’ were increased by two rak‘ahs. Fajr was confirmed as two rak‘ahs so that one could recite at length in it. Hence the Prophet (blessings and peace of Allah be upon him) used to recite at greater length in it than in the other prayers. Sometimes he would recite Soorat as-Saaffaat in it when leading them in prayer, as was narrated by Ahmad (4989) and classed as hasan by the commentators on al-Musnad. Sometimes he recited Soorat ar-Room, as was narrated also by Ahmad (15873) and classed as hasan by the commentators on al-Musnad. Sometimes he recited between sixty and one hundred verses, as is agreed upon (by the hadeeth scholars). So as to allow lengthy recitation in Fajr prayer, it was confirmed as two rak‘ahs, as it was enjoined in the beginning, not because two rak‘ahs were dropped from it. 

Shaykh al-Islam Ibn Taymiyah (may Allah have mercy on him) said: 

When Allah, may He be exalted, enjoined the five daily prayers in Makkah, he enjoined them with two rak‘ahs each. Then that was confirmed when travelling, and more was added to the prayers when staying at home, as is proven in as-Saheeh from ‘Aa’ishah (may Allah be pleased with her), who said: When he (the Prophet – blessings and peace of Allah be upon him) migrated to Madinah, (two rak‘ahs) were added to the prayers when staying at home (i.e., not travelling); Maghrib prayer was made three rak‘ahs, because it is the Witr of the day, and Fajr prayer was confirmed with two rak‘ahs, so as to allow for lengthy recitation therein, hence there was no need to increase the number of rak‘ahs.

End quote from Majmoo‘ al-Fataawa, 23/114. 

A similar case is the shortening of Jumu‘ah prayer to two rak‘ahs because of the khutbah. Ibn al-A‘raabi narrated in his Mu‘jam (1447) that ‘Aa’ishah the Mother of the Believers (may Allah be pleased with her) said: Allah, may He be exalted, enjoined the prayer upon His Prophet (blessings and peace of Allah be upon him) in Makkah, with two rak‘ahs in each prayer, except Maghrib, which is the Witr of the day. When he migrated to Madinah and settled there, two rak‘ahs were added to each two rak‘ahs, except Maghrib prayer, for it is the Witr of the day; Fajr prayer, so as to allow for lengthy recitation therein; and Jumu‘ah prayer, in which the prayer is two rak‘ahs because of the khutbah. 

Ibn Qudaamah (may Allah have mercy on him) said: 

It was narrated from ‘Umar (may Allah be pleased with him) that he said: The prayer was made shorter because of the khutbah. The view of ‘Aa’ishah is similar to that. Sa‘eed ibn Jubayr said: Jumu‘ah was four (rak‘ahs), then the khutbah took the place of two rak‘ahs. End quote from al-Mughni, 2/224 

And Allah knows best.