Board Thread:Assassin's Creed general discussion/@comment-26314858-20150714112803/@comment-2112031-20170515160711
I have my own theories on this as well, and if I recall, the precise statement was: "May the Father of Understanding guide us." Translated exactly in that manner as well.
It is my understanding that this refers to God, as the Templars appear to be religious individuals and if you consider that the Knights Templar were Christians then this stands to make even more sense. I don't think the Father of Understanding is a concept, but more an admission, or some sort of prayerful remark. The Templars during Rodrigo's time as Grand Master were also Catholics, or were implied to be Catholic, I mean, Jacopo was a pope, was he not? Rodrigo still believed in God, just not in the traditional manner of the Catholic Church at the time, and Ezio was raised a Catholic as well. Many Templar sympathizers, and Templar adherents were religious, so it stands to reason that the Father of Understanding refers to God. Strangely enough, I don't recall if this appears in other games as well, or merely just AC2.
Some of the Templars are religious, but the organization as a whole is not. Most of the Templars were aware of the Isu and, as such, tended to be wary of myths and religions in general.
Neither Ezio nor Rodrigo were believers. Ezio explicitly identified himself as a non-believer in Discovery and Rodrigo very clearly stated that he did not believe a single word of the Bible, only becoming Pope in order to gain power and access to the Vatican Vault.
As for the Father of Understanding, I personally suspect that it might be Cain, given that his mark was used as the Templar insignia. We can't really know until it's revealed.