While I consider the Minutemen to be the "good" faction, since they only care about helping people with no hidden agenda, they're just extremely poorly organized and ill-equipped.
The Brotherhood has returned to its roots and has become far more cold and militaristic since Fallout 3, acting with brutality and extreme prejudice towards anything they perceive as a threat. In light of that, they are easily the most advanced, organized, and powerful faction outside of the Institute.
The Railroad are sympathetic towards synths, but don't seem to have any long-term goals beyond that. They also don't seem to want to extend their help to every day people, and have poor organization and numbers.
Institute is a complex one. They are far and away the most advanced faction, but have very questionable ethics concerning treatment of wastelanders and generation 3 synths. It also doesn't help that it's never really clarified why they would need their slave workforce to be as close to human as possible, and then deny them any sort of rights.
I personally went with the Brotherhood. While their methods and motives can be very harsh at times, they have the drive, technology, training, and organization to make a tangible difference in the state of the wasteland. They also are generally more of a help than a hindrance since they happily kill super mutants, feral ghouls, and other mutated creatures, making life that much safer for wastelanders.
"They asked me how well I understood theoretical physics. I said I had a theoretical degree in physics. They said welcome aboard."