Re: Us fighting the Brotherhood: The Institute is meant to be one of the most technologically advanced places left in the world. Remember, only the D.C. Brotherhood is made up of nice guys. The rest of them are mostly assholes.
We'll likely have a New Vegas-style choice between supporting the Brotherhood and taking over the Institute, or siding with the Institute's scientists and androids (in that same video montage, there were enemies labeled "synth") to keep their technology safe and secret.