Except for the fact that you don't have access to the technology or the techniques required to do that. If the Mechanist, who is infinitely better with robotics than our characters are, had to use the pre-war brains found in the facility, what makes you think you can magically do it?
Like I said, headcanons (Which mean nothing in terms of the actual story) aside, the correct and most logical answer is that we are using the brains in the facility.