NOTE: The following is my own opinion, I cannot stress this enough. Do not grill me about my opinions unless you're just looking for attention.
A lot of people share the same opinion, which is that The Institute is the most evil faction in the Commonwealth. In truth, especially if you side with them, the Brotherhood of Steel is.
The Institute has, and always had a sole goal to achieve; the preservation of mankind, and it's future. They only seek to save everyone in the long run, even if it means doing research that many find taboo, such as experiments with the Forced Evolutionary Virus, or the enslavement of synthetic humanoids believed to just be machines. They at least have good intentions.
In contrast, the Brotherhood of Steel will destroy anyone who they believe possesses any old world technology, especially technologies that they lack. They claim it's to protect people, and that they will eventually use the technology to rebuild what was lost during the Great War, yet all they actually do is hoard all of the technology and research it. They don't genuinely care for anyone who isn't among their own faction, and they seek to destroy all who aren't human, even if they have more humanity than normal humans. (Synths, rare Super Mutants often dubbing themselves as Meta Humans, etc.) If the Sole Survivor chooses to side with them, and has Madison Li help fix Liberty Prime, the Brotherhood destroys one of the last factions that actually displayed hope for all of mankind, and Li will leave the Brotherhood once more, as she believed her peers at The Institute did not deserve the destruction that the Brotherhood brought down on them.
The Institute may treat their synths poorly, but that's simply because they don't realize their true potential and how similar they truly are to organic humans. If the Sole Survivor chooses to side with them and becomes it's Director, some of the staff even encourage him/her to make improvements, which could imply that the future of The Institute would mean that Synths would have just as many rights as normal humans, and would be treated the same as the rest of the human race. That would essentially turn the whole "evil" argument onto it's ass, as one of the biggest reasons people label The Institute as evil is their enslavement of what they believe to be humans, but at the time, they were believed by their creators to just be machines.
Lastly, I'm sure many have heard the following phrase:
"The end justifies the means," which means that even if you do wrong, if it's for the right cause, it's justified.
The ends that The Institute work for is to save humanity using the research and technology that once destroyed it, and pretty much preventing the Great War from being repeated by eliminating the need for war.
The Brotherhood of Steel basically slaughters The Institute for their technology, and simply because they believe synths to be a menace that deserves to be eradicated. They don't actually seek to help anyone, just destroy what they see as threats to their own strength. The Enclave was a threat that had to be destroyed, as they pretty much were pure evil, but in this case, the Brotherhood is dead wrong.
In short, in my opinion, if you seek to destroy The Institute, you should really rethink your decision.
The Minutemen wants to defend everyone but can't, as they're completely outnumbered and generally outclassed when it comes to skill and equipment.
The Railroad wants to free the synths and destroy their creators who are "enslaving" them, and give the synths "normal" lives, even though they will never truly be able to live the same lives as us. (Not to mention if they unknowingly place the memories of a serial killer into a synth body, they just revived a very powerful murderer who will resume their spree)
The Brotherhood of Steel initially had good intentions when Roger Maxson formed it, but in the more recent years, especially in the Commonwealth and Mojave, they've become selfish and corrupt. They're basically raiders that don't slaughter everyone, but still raid everyone for their technologies. On top of that, they don't believe synths should even exist, and want to eradicate them, even if they have actual emotions and humanity.
The Institute may do wrong, but they have the resources to literally rebuild what was lost in much less time than any other existing faction. If you destroy that, you could set back humanity's progress by a huge amount, if not destroy it's chances of ever recovering from the Great War.
In my opinion, The Institute is the "best" faction in Fallout 4.
Aside from all of that gaff, the "karma" of any faction really depends on the Sole Survivor's choices and ideals. Though no matter what, I personally can't ever see the Brotherhood of Steel ever being a good faction. The only time they've ever really been good is when the East Coast Brotherhood run by Lyons was focused on helping the people of the wasteland rather than bullying them for their technology. The other Brotherhood factions are obsessed with having the best technology, and will destroy anyone who has better technology than them. I see them to be almost on the same level as the Enclave in terms of evil-ness.
