The Brotherhood of Steel wants to destroy all rogue technology.
The Institute wants to transform the Commonwealth into something good by razing it, essentially. The Railroad wants to help Synths escape the Institute, because they see Synths as being human beings. 3 factions are in direct competition with one another. We are presented with 4 factions in the game. I find myself EXTREMELY frustrated with the writing, or lack of writing, in Fallout 4. This tends to leave the audience feeling manipulated and frustrated. When poor writers try to include moral grey areas into their work, they usually have to resort to pulling strings to set up JUST the right situation for there to be no right answer. If you're not Alan Moore, you should probably not even try it. The problem is, it's INCREDIBLY hard to pull off. Take it as a product of our modern times, and a feeling of a lack of moral absolutes, but I feel like writers are tripping all over themselves to include these belief systems in their writings.
I feel like, when it comes to writing and storytelling, there is a fairly pretentious modern trend of living in 'moral grey areas'. I have spent about 75-100 hours in the Commonwealth and while my intial thoughts were extremely positive, the last dozen or so hours have been so poor that it really soured my opinion on the game entirely.