I also would suggest a mod to solve the "kill everithyng" in a more realistic way. For the Brotherhood I think a questchain should be implemented where you rise from a stranger to a real counselor for the Brotherhoods behaviour in the Commonwealth. I think it is not necessary to gain control over the Brotherhood but to give them limits in the way they interact with other fractions. There are console commands to befriend or daemonize fractions, so that should be possible. For the Institute it should be similar. If I am director, my way is the way to go and if the members of the Institute do not listen, there are the Minuteman or Brotherhood who can be installed as executive of my will. Another way could be to bring the Institutes members to a point where they see how inhuman it is to kidnap people and replace them by Synths. I also would like to accept them their creation, the Synths as new form of intelligent life, maybe allow them to emigrate to a new settlement where they can advance themselfes further. And finally the Institute should use their ressources to research solutions for radiation damage, the Supermutant cure and body part/organ replacements to cure diseases. All those things would in my opinion be ways worth a highly educated and ethical superior kind of people. All thats implemented now into Fallout 4 is a (un)subtle way to tell every player conscious and subconscious - violence is the way to settle all problems and differences in the world. Which is just wrong, because force always leds to counterforce as everybody can see in the middle east. The destabilization of Iraq because of political lies drove a whole section of the planet into countles wars and terror. All just that some militant and weapons producing and exporting countries can rise their economic growth - an illusion if all is summed up.