Thats because the Bethesda Fallout games are based long after the original ones IIRC,meaning all the control Vaults would have opened on time,ie,less than 100 years after the Great War,meaning the remaining Vaults would be the ones set aside for experiments and remember the control Vaults would only need to be a tiny sub-section of the entire Vault network since The Enclave/Shadow US government already had their own Vaults and bases in parallel,and all they wanted was to take their people and run away to another planet.
I don't agree with this entirely - if you have decent Charisma and other perks you can usually talk yourself out of situations without violence - done it many times in Fallout 4. However,you still need to consider this a destroyed world with people barely surviving - look through human history,it was not that uncommon when resources were short for people to start fighting and killing each other instead of working together.
In fact,my biggest gripe with the Bethesda ones and even the old ones is the finality of the endings if you finish the main story line. In almost all cases,you NEED to side with one type of faction against another type of faction. What would be nice is that you could try and negotiate a settlement or peace between factions,or even have them in sort of cold war state or even destroy all of them.
You can see this with having to destroy The Enclave in Fallout 2 and 3,the fact you could not negotiate between any of the factions in New Vegas,and I doubt its any different in Fallout 4. I mean the whole series has missed a trick in allowing you to explore The Enclave - in fact The Remnants in NV were the closest to doing that.
You might be an "agent of change" but a very limited one at that.You still need to kill and destroy at least an entire faction in all of them. The only way not to do is to try and avoid playing the whole main stories of the games,which means a very black and white choice.