People have typed these already, but I have to chime in here:
1. Playing through NV again, which I started toward the end of finishing Fallout 4. In NV, there are four factions. One, the Legion, is the sociopath's/objectivist who doesn't understand the concept of Darwinism's faction. If you're playing as a dick, that's where you go.
The other three are shaded very finely so that picking between them forces some thought. House is a benevolent dictator, but he's still a dictator, and he has no vision for rebuilding the region beyond New Vegas. Is what House is doing good enough for the region?
The NCR is an unwieldy, bureaucratic regime, but they are the best chance at creating stability in the West/Southwest. They genuinely are working toward becoming a strong democratic republic and will use Hoover Dam to supply power to people who otherwise would be SOL since they can't get into Vegas. However, are they reason enough to forcibly overthrow House and what he has built?
Yes Man foments an overthrow of House and an avoidance of the NCR's direction. Freedom has a high value and New Vegas deserves the chance to build its own goverment just as Shady Sands did in earlier Fallout games, but what if New Vegas falls? What if they can't control the Dam and its potential for power is never fully exploited (or worse yet, they can't protect the Dam and it is destroyed)? Is allowing New Vegas its freedom worth taking the risk that they fail?
Meanwhile, in Fallout 4, we have the Institute, which never quite tells you what their end game is, but which we know experiments on and kills people. The Railroad, which has a noble goal but no plan for the region beyond "save synths from the Insititute," and the Brotherhood, who are back to being the paranoid nutters that they used to be, but who seem to be more "violent militaristic Luddites" than "paranoid and secretive tech librarians" in this game, as if the FO4 team played 2 and NV for reference, but went a bit too far in the characterization.
Then there are the Minutemen, a less-fleshed out and fledgling NCR. Easily, this group is the most reasonably defined of the four, but other than the intentionally ridiculous Legion, they aren't written nearly as well as any other group in NV in terms of their motivation, etc.
2. The reactor in the Institute. It's generating power/producing clean water for the region. Why would anyone blow it up?! Even if the RR is disinterested in doing anything in the region beyond subsistence living and saving synths, they could still do something genuinely good in providing water for the region. The MM SHOULD DEFINITELY want to keep the reactor going! They're a group with ambitions to reclaim trust from locals and power in the region. Keeping the reactor going is a clear win-win for them!
The Brotherhood are generally about as eloquent and rage-filled as your typical Super Mutant in this game, but even for them, blowing up the reactor would be dumb because they're destroying all sorts of tech that they could be preserving or studying, even if some of it has been updated by the Institute.
Why wasn't there an option to save the reactor/not kill the scientists/just kill the Gen 1+2 synths guarding the Institute? Even if one has to pass checks to get the leaders of whatever group you align with to go through with this plan, it would make sense. You get the reactor, the credit for bringing clean water to the region, AND a bunch of scientists who now work for you and who can continue to rebuild the Commonwealth.
3. Why the fuck do the MM want to wipe out the RR? I didn't get that request, but I did see others have it. In fact, why can't we, through Charisma/Persuasion checks, align those two groups? They seem to have a vested interest in order and freedom for humans/Gen-3 synths and would make for a feasible coalition government in the area.
In fact, not having the chance to align groups was a shame and would have been a clear narrative upgrade over NV (where I don't think aligning groups was feasible since they were all cross-wise to one another in terms of what they wanted for New Vegas/the Mojave).
I could go on, but I've written WAY too much already and apologize for the long post.