I came across some ahadith which said Imam Ja’far, and by extension God, loved his son Isma’il more than Imam Musa.

Saad bin Abdullah Ashari has narrated: Narrated to me Abu Hashim Dawood bin Qasim Ja’fari that: When Abu Ja’far passed away, I was present with Imam Hadi (a.s) and previously the Imam had hinted to him. Therefore, I thought and said to myself: This is just how it happened in the case of Abu Ibrahim [Imam Kadhim (a.s)] and Ismail Ibn Ja’far that when Ismail passed away, Imam Sadiq (a.s) publicly announced his death so that no one may say that Ismail or his descendants are Imams. Imam Hadi (a.s) came to me and said: Yes, Aba Hashim, change of destiny occurred (Bada) with regard to Abu Ja’far and Almighty Allah replaced him with Abu Muhammad as He did in the case of Ismail, son of Imam Sadiq (a.s), after Imam Ja’far Sadiq (a.s) had declared and mentioned him to be the Imam after him and appointed him as his successor; just as you said to yourself, although it would be displeasing to the followers of falsehood. My son, Abu Muhammad is my successor and he is having all that which the Shia society is in need of and he is having the distinctive signs of Imamate, by the grace of God.

Kitab al-Ghayhah > Hadith 167

1) How could Isma’il be more beloved, when he is just a (though virtuous) fallible human, while Imam Musa SWSA is the Infallible perfect being, who existed before Isma’il and was still the Imam SWSA before the creation of both creation and Isma’il?

2) The Imams are pre-existent, so how then could Isma’il Ibn Ja’far as-Sadiq and Muhammad Ibn ’Ali al-Hadi have had bada’ in regards to their Imamah done in life, when Imam Musa SWSA and Imam al-’Askari were still the Imams before creation? As Kitab al-Ghaybah 167 clearly says God replaced Muhammad Ibn ’Ali al-Hadi with Imam al-’Askari.

3) How do we reconcile this with the true nature of the Imams? Or all these ahadith fabricated?

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1- Assuming these hadiths are authentic (the Imam really said those words), then one meaning is that he is speaking about pure human emotions. Ismail was older so Imam Sadeq (a) had more human memories or him, so emotionally he was more attached to him. This is very natural. Sometimes a person can have two sons, and he knows one is much greater than the other, but since he spent more time with the lesser one, he feels a greater emotional connection to him. And at the end of the day the Imam had human emotions too.

2- Here Bada’ means Allah revealed to the people, not the Imam. Imam Sadeq (a) knew very well who the next Imam would be, but the people didn’t. They thought his eldest son Ismail would be, so Imam Sadeq pretended to go with the flow here just to prove to people that Allah chooses the Imams—not him, because if he were to choose, as a father and as a human, he would have chosen Ismail. But the point is that Imams don’t do things out of human nature—they do everything by divine command.