Except the plan wasn't to have you live there as such. They didn't want the SS to infiltrate them, and Father just wanted to see what his last remaining parent was like and who they are, what they would do in situations. He never expected you to hunt the Institute down and take down coursers single-handedly. As Father approached the end of his life, he wanted to see his remaining parent released from the cryopod. It was a gamble whether the parent would survive or not, but at least Father could die knowing what his parent was like.

Also, the Institute hires Kellogg because he's reliable. Kellogg is harder to kill than a courser and being that Kellogg has Institute technology that prolongs his life Father even states that they are keeping him on a leash. If Kellogg was to be released, the Institute would suffer and so would the Commonwealth. Kellogg killed Shaun's Mom before Shaun even became Director, Shaun even shows disliking for Kellogg, but the Institute use Kellogg to go on missions coursers couldn't do. When Kellogg shoots Nora and steals Shaun the first Gen 3 coursers weren't even created. From what I can tell, Kellogg has less work given to him by the Institute being that coursers can take the small jobs like reclaiming synths.

Just because a faction claims they mean no harm doesn't make it true. The factions in Fallout 4 all believe they mean no harm and are the saviors of the Commonwealth, which is not exactly true. In truth, the BoS used the Prydwen to strike fear into the Institute, and you can even bring this up in dialogue with Paladin Danse. The BoS believe they are fighting against technology run amok when from a Railroad perspective they are killing innocent people and from an Institute perspective they are preventing the production of advanced technologies that mankind can use to revive itself from the state it is in. Personally, I liked how morally grey these three factions were and I myself end up torn between all three. I do think Bethesda ruined it though by adding the Minutemen, a two-dimensional faction that serves no purpose other than radiant quests and a backup ending. I bash New Vegas a lot, but I actually liked Yes Man and I found myself siding with him in most of my playthroughs. In Fallout 4, I usually just side with BoS or Institute and build up the Minutemen as a side questline. The Fallout 4 storyline would've been better off if they left the three factions as it is and detailed the Railroad slightly more to make their cause seem more tempting. The only reason to side with RR is for ballistic weave. I quite liked how shady the Railroad were depicted in Fallout 3, but in Fallout 4 it seems as if they are known by every NPC in the Commonwealth.

I don't believe that kellogg was more lethal than coursers, he even stated in the questline that he feared them. His usefulness would have benefited the institute prior to Shaun taking over, but once he did take over it and the Gen 3 synths were created he definitely became obsolete, this is proven when you fetch the chip from the courser and the courser just shreds 30-40 gunners like they aren't even there. Obviously neither of them are worth a crap if some prewar vault dweller can breach the most secure facility in existence.

I think the brotherhoods intimidation was pointless, considering they have absolutely no way of getting to the institute, they don't know where it is or how to get to it without the SS who as far as the game is concerned can be as completely retarded as humanly possible and gain control of most of the major factions in the game.

While they have their own goals, I think they were portrayed terribly. The brotherhood is injected on you just like the minutemen very early on. The Railroad is just some crappy faction that you encounter on your forced road with either of those factions which you somehow depend on in order to get to the institute. All around it was all terribly written, if he wanted to see what his parent was like why would he wait 40+ years to bring him/her out of their cryo slumber, getting to know someone over a period of days means little to nothing not to mention you can choose to kill your own son lol.. the whole point of the game was to get him back, yet you can kill them all.

Yes, you can avoid the Fallout 4 story, after the news broadcast, do not run to the vault, run straight out to the bridge near sanctuary past the tank, there, you will get nuked in the face and the game ends.

In all seriousness, if you were talking about kellogg, yes, it was avoidable but then the developers would want a story about vengeance, if you, your spouse and your child is alive, you would a) get frozen forever until someone discovers you or b) become a settler.

You would think the writers would have at least acknowledged a possible merciful route. If there was more RPG elements you could have convinced Kellogg to tell everything he knows about Shaun in exchange for letting him go free and unharmed. It would also be a big surprise to Father as he would not understand why you spared Kellogg and therefore adding more depth to the story overall.

Lol in all honestly there's such a disconnection in the story when I found Kellogg as easy as it was I didn't even care if he died or not nor did I care that he shot my spouse. When I found shaun I didn't care that he was part of the institute, there's no connection to anything in the story which is why it was terrible. You had a connection in New Vegas (someone shoots you in the face XD), it doesn't force you to do anything and the factions have tons of various content all around the mojave to form attachment to one of the various factions around the mojave.