First of all, let us assume that Fallout 4 is set in Boston, for the sake of this thread. We know that Dr. Madison Li ended up leaving the Capital Wasteland and went up North to the Commonwealth/Institute. I am pretty sure she will have a role in Fallout 4, if it's indeed set in Boston. What I imagine now is that she somehow climbed up the hierarchy or otherwise assumed total control of the Institute and now commands a legion of Cyborgs and Androids - ready to do her every bidding! A powerful, evil force of destruction! Even though this behaviour doesn't reflect her character in Fallout 3, I think it would be cool. She is now the evil supervillain, so to speak. Totally corrupted by power. A dragon lady dictator! What do you think about that? There is just no way around her not having a role in Fallout 4, if it is set in Boston. And this role would be something no one would expect; you know, instead of just a lame minor encounter.