Since release I've spent a lot of time on this board listening to the various pros and cons (all passionately argued) and compared it to what I saw in game. And at the end of it I went with the Minutemen for one reason:
I just want to be left alone.
What the other three factions all have in common is that they each have an agenda they want to impose on everyone else. And they're all willing, even eager, to use violence to impose it. No real thought is given to the normal people who just want to live in the commonwealth and not be bothered with their synths, nuclear bombs and giant robots.
So I wiped them all out. Hopefully they got the message that the Commonwealth will not be their playground or their battlefield. And if they want to come back I've got plenty of ammo left.