The institute synths are ticking tyke bombs, a simple word or phrase and they can go hostile on you, chances are the institute could send out a frequency and BAM all synths everywhere become horrible monsters willing to gut you in the night.
The BOS is right to want to eliminate them, and ghouls have the same issue but its much less profound they can degrade under the right stress and pressure. Only individual ghouls with strong will power remain sane for long periods of time.
Super Mutants also degenerate with time as we can see in Nightkin, with the majority being dumb evul.
The only gripe with the BOS is that they send everything from little children to a highly vulnerable airship to a foreign land to take out an organization of pre-war learning.
I'm iffy about the BOS, Minutemen, and Institute. The BOS message is legit, but they sacrifice freedom and endless potential, the Institute is cold and willing to wipe out entire settlements and cities for practically dam reason, but they can reverse engineer or engineer miracle cures for the FEV and pre-war conventional/engineered diseases. Relay tech is also incredible, sooner or later hardlight tech might come into play. As director you can changes a whole lot as Maxson changed the BOS.
But as with Elder Lyons once you go, or get assassinated they'll return to their genocidal maniac roots. And possible lead the new world into the ground. As they did to the United New Commonwealth Settlements and countless others.
The Minutemen are vulnerable and too weak to be a long lasting game changer, but they stand of independace and freedom for today. And its always nice to directly impact lives. However, a single synth infiltrator and the house of cards comes tumbling down. Like the Quincy massacre.
The Best Hope is the Institute, the most reliable hope is the BOS who after 200 years have always kept the wasteland safe if at the cost of stagnation.
Calculator
Master
Enclave
The BOS has been through it all, IMO the NCR beating them shouldn't be canon in the original Fallout 3 the NCR get whooped by the BOS after all.
For the NCR supporters out there look no further than The Divide, Vault 22, and the massacre of intellectuals of the Enclave, BOS, and Followers of The Apocalypse, rather than incorperation the NCR take them out. Even Ceasar's Legion came from the NCR. Had the BOS won their war against the NCR there would be no Divide, no change of spreading of Vault 22's spores, and No Legion. The BOS are also smart enough to place a plug on Elijah who can end all life in the mojave. They have the right ideals to an extent, but simply needed to recruit outsiders sooner rather its too little too late for them now.