User blog comment:Suparockr/List of Plotholes throughout the series/@comment-3228423-20120719022353/@comment-24174486-20120719023903

I always saw it as the Catalyst being able to read Shepard's mind. It chose a figure that it saw was prominent in Shepard's psyche to represent itself. That is not the only thought of Shepard's that it acknowledges, and there are other cases of "mind reading" in the ME universe.