Lead narrative designer Mary DeMarle says:

“Yes and no. At the start of conception, we weren’t sure what characters from the original game would play into our story. We only knew that: 1) we wanted to make a prequel; 2) the plot should involve an Illuminati-driven conspiracy aimed at controlling mankind’s evolution (aka transhumanism); and 3) our hero and main villain should be completely new characters. As we developed the conspiracy itself, two more elements became clear: 1) each  aspect of the Illuminati’s plan needed someone to be in charge of it (this is why we ended up creating Taggart and Zhao, for example), and 2) that the Council would not have trusted any of these new characters with overseeing their ENTIRE plan. At that point, it was pretty clear that Bob Page would be involved in the story.

So yes, we knew he would be involved long before the entire plot was figured out, but no, we didn’t know immediately how or why. J