Pair the Railroad with the Minutemen. That's the best ending given to us since the other 2 factions are inherently "evil." Ultimately, the RR isn't entirely opposed to helping the people of the commonwealth; Deacon is willing to, and once the Synths are "free" the RR has lost its purpose - you'll have an entire clandestine organization full of people that once dedicated their lives to aiding synths now without purpose. Its not too far-fetched to see the general of the minutemen using the successor of the RR as its more undercover wing. Ontop of that, siding with literally anyone else than the RR is to stand by and be "okay" with genocide/slavery. The brotherhood would murder all synths and ghouls and the minutemen on their own are a reflection of the Commonwealth which has a strong prejudice against Synths. Problem with the institute is that there is no way the members of it would ever be cool with you just liberating the synths, ending the synth program, or suddenly redirecting the Institute towards assisting the Commonwealth - you would lose all legitimacy as director amongst the Institutes board.
