Thank you.
The Minutemen get harshed on a lot, but they're also the bravest of all the factions.
A citizen with a laser musket stepping up to form ranks, no matter the cost. They have the most to lose and the least to gain, individually. Yet they're doing their duty. Effective or not, that's courage. If the Sole Survivor supports them, this collection of farmers and citizen soldiers are the ones who bring down the big bad Institute... not all the pretty knights in their airship, not the collection of super spies and heavies.
Joe Dirt, his laser musket, and a bucket full of gumption. That's a lot more endearing, IMO.
Also, they're the faction with the real plan on fixing the Commonwealth. The BoS are next in line with providing security, but the Railroad even admits they got nothing and the Institute just waggles its fingers and goes "TECHNOLOGY! OOOOOooooooOOOOooooo!" as if that'll magically fix things (and they're BSing anyways -- their plan is to Enclave it up and wait for everything on the surface to die and then replace it).
The plan that works, that's practical is this -- give people food, shelter, water, and security. You give people those things and the world gets a little bit better every day. Every day that a farmer can feed his kids and not fear a supermutant attack, the world just a bit better. Every day that clean water comes out of a pump or purifier and a farmer can trade his excess crops for things they need like medicine, clothes, etc instead of paying tribute to raiders, the world gets a little better. Fixing the world isn't magic, it's hard work, dirt under the fingernails, about a million gallons of elbow grease, and dedication. It fixes itself in increments and fractions, not magically with a wave of a synth. With peace of mind at home comes extra resources, with extra resources comes trade, with trade comes agreements and organization, with that comes government and democracy.
It may take a hundred years, but it works.
In a perfect world, the Minutemen end standing guard over the Commonwealth, the Railroad stand in the light without fear, knowing their job is done, and the Brotherhood can go home, with no more enemy to fight, and go seek a new enemy that their might is truly needed against.
As for the Institute, to answer your leading question (since this is a spoilers forum) --
While the Sole Survivor, if they take over the Institute, can take a reform oriented approach and even a positive tone with the world above, the prevailing sentiment when you first enter the facility is that the people on the surface are un-people. They are all dead men walking, so there is no point at treating them with any respect, and it's best to get use of them while they can as guinea pigs.
This is not a mentality that you're actually able to change in game -- you can state that you're going to be helpful and redirect the director's personal resources to helping the surface, but you can't force the Division Heads to to do the same (you're not a dictator, just the head of the board of directors). Justin Ayo, acting head of the SRB, and Dr. Zimmer (SRB head on sabbatical) are especially odious. You also have no way, shape, or form to release or free the Gen3 synths currently in service to the Institute, and you have to acknowledge their status as property.
The Institute seems to be a more sterile version of the Enclave. They are not as proactive about wiping out the Wastelanders, but are willing to let decay and inertia work their magic. Part of why they want the nuclear reactor they are working on to be completed so badly is so they can ignore the surface even more than they do now, as they don't want to be pulled into the Commonwealth's death throes. At the same time, these are the same people who used a strain of FEV they had from the War to create the first Commonwealth supermutants and then released them into the wild to 'see what would happen'.
Yeah. That's not morally indefensible at all. (/sarcasm)