User blog comment:D. Cello/Assassinews 10/11 -- Desmond's Ancestry Revealed/@comment-1884750-20111013230537/@comment-3310127-20111014022512

For your first point about Eagle Vision, it is true it is an inherited trait. But it is very possible that Ezio and Altair had inherited it from different Those Who Came Before. As for humans having the ability:

             "Though every human held the potential for it, bloodlines of humans who interbred with Those Who Came Before held a greater concentration of the necessary genes, and were thus more likely to exhibit the ability."

There isn't one TWCB. There were a fair number of them. So it is possible two lineages of TWCB (Altair and Ezio) became one lineage (Desmond).