Aside from the obvious android-driven plot, I also have a feeling we are going to get some psyker stuff, I mean the Institute is this mysterious faction, they're bound to have a secret like this. Also they remind me of the Second Foundation, that's the other reason why I have this feeling, though that's probably just wishful thinking that Asimov's works might be an inspiration for a Commonwealth game or DLC. I also advise Bethesda against portraying the Institute and their tech in any way similar to how Obsidian portrayed Big MT and their tech. Don't get me wrong, I like OWB as much as the next guy, but still the robot and the dog disappearing to make a cyberdog is not the kind of science the Institute should have.
edit: Before anyone would say it, the Commonwealth is not confirmed as a location for F4, so this topic can stay as is, imo.