That's a great question and I don't know the answer. maybe once I've been through the ending sequences I might have a different perspective. As it stands now I'd probably guess that exactly what I am setting up would be it. But there are plenty of holes in this argument, not least of which is the Minutemen are a weak faction. As I said earlier I can't imagine these people having any long term success without my help. Too disorganized and they have no special tech to help them (that I've seen), unlike all the others.
The problem for the Railroad is that if the Institute is indeed destroyed, the Railroad loses its purpose, and would probably fade away.
BoS is a good candidate, but too extreme. But I might have thought the same about the Enclave, and their ending was canonical in FO3.
The Institute is evil, right? That's what everyone says but I have not dived deep enough to really see this, it's more a hunch as I talked about earlier, born of a lifetime of suspicion and mistrust in others
To achieve anything in this game you must be prepared to dabble in the boundary of disaster — Stirling Moss