FO4's settlement system is usually what causes the most salt in my experience, since it adds a truly stupid amount of responsibility to the player. This is coupled with how the settlements are populated by some of the most brain damaged, paste eating retards to somehow survive in the wasteland.
My thought was that you should only have had to deal with micromanaging and building Sanctuary Hills, and while you could help secure the other settlements, they would grow and expand on their own without input (three tiers of development, each getting stronger and granting more resources).
Guys, I just wanna find my son, not spend my days being governor of a chunk of nuked Massachusetts.
Fallout 4 has a really bizarre story because I think it works very well if you play as a male Sole Survivor and focus almost exclusively on the main story missions. However, if you play the game in any other way, it gets extremely weird very very quickly.
The reason I say that the male works is that his background is canonically as a soldier, so him jumping into a power suit, picking up a mini-gun, and killing waves of raiders as well as a deathclaw when you get to Concord works pretty well. The female, however, is a lawyer who in between studying for her law degree also apparently went to the shooting range as well as read up on basic power armor operations and has absolutely 0 issues with murdering dozens of people.
As you pointed out, delaying the story missions or putting them off to do other side content makes coming back to them play out nonsensically. "WHERE'S MY SON?!" Nate screams, as he reloads the laser sniper rifle he bought at the marketplace he spent several in-game months setting up. "MY BABY'S BEEN TAKEN!" Nora cries, before preparing to explore a heavily defended mine shaft for absolutely no reason other than 'its there'.
Whether its capturing settlements from supermutants or convincing a bunch of robots that the water supply is good, any side quest you undertake only further the tonal dissonance from the voice acting when you eventually do get back to the main missions.
Also while I'm bitching about the game, Fallout 4's randomized loot system is bullshit. When you explore a collapsed building and unlock a safe that presumably hasn't been opened for 200 years, you have to ask yourself why the previous residents felt it necessary to protect a gun they build out of piping and a typewriter.
Also Super Mutants in general.
The Master is fucking dead and no one is making any more. From Fallout 1 to Fallout 2, there's a dramatic drop-off in Super Mutant population, and by New Vegas they're mostly relegated to 2 tiny points on the map, Black Mountain and the Jacobstown. But Fallout 3 & 4, even though they're on the opposite side of the continent, is just swarming with Super Mutants. You can't take 20 steps without running into one. They can't reproduce and have to be individually created, they shouldn't exist!