I disagree with the majority of what was said in the OP, however I appreciate there's a good few points that are subjective. FO4 has been quite a disappointment for me, and whilst not a terrible game I feel like it's not as good as the previous gen FO3 and FO:NV (particularly FO:NV).
Settlements - I really don't care for them. I never asked to become what amounts to mayor of multiple towns, and it annoys me that by following the main quest you're always handed Sanctuary where people look to you as the leader whether you like it or not. As an extra little feature, sure whatever, but it should have been entirely avoidable if you didn't want to do it. Making every character I play an obligate community leader is one of the many ways Bethesda failed to allow for you to have roleplaying distinctions between the different characters you play.
Beautiful world - It's too colourful for me, I find it hard to believe after 200 years baking in the sun everything would still look so vibrant. I also don't like how every vault looks as shiny and chrome as Vault City, one or two could look like that sure but they should have definitely given more of them a dank aesthetic like previous games. Again, entirely subjective but for me it really didn't work.
Enemy level balance - I find the combat too easy, even on Survival and even around the earlier levels (I'm level 25 currently). This is going melee which is supposed to me more difficult as you have to close the distance with enemies and tend to get shot at a lot. Again this is subjective, I know many people find the game difficult.
The crafting - For me I find the weapon crafting way too much, and I think it's entirely unrealistic that everything you pick up can be modded like crazy. Were the original manufacturers of these weapons so incapable at their job that they couldn't produce a single weapon that was good enough as is? I appreciate that crafting allows for a way (with the perk levelling restrictions) to organically access better weaponry as you level, however FO3 and NV already had a system for that as weapons only became available at vendors when you hit a certain level.
I much preferred the simplicity of NV's mods to FO4's, and personally I feel like having a more honed selection of equipment your weapon choice in NV was perhaps more distinctive than a system where you're always going to pick up the most damaging weapon and as there's no restriction on how high you level you're always just going to get the best mod for it in the end. When you couple this to a perk system that improves damage with all weapons equally (no more Cowboy, or Pyromaniac, or whatever) then your weapons system is now much more convergent than what was there previously.
In terms of armor crafting, I don't have the same problem with it as it allows for a lot of aesthetic customisation and what's best for armor is at least a bit more debatable.
The interface - I like the interface, I much prefer a clunkier yet completely functional interface that allows me to do exactly what I'm trying to do than one where the developer over simplifies and completely fails. I would love it if Bethesda forever left the interface as is.
Freedom - I don't think this is true, your character harps on about his son and his dead husband/wife so much that to avoid the issue feels awkward when they're so vocal about it. Whilst you can do whatever you please, Bethesda unfortunately have made it feel wrong to do so. They also assume whatever character you play would care about his family - what if your character had been having an affair and wanted to ditch their spouse and kid? If we compare this to FO3 which had the same premise of tracking family down more or less, then there is a system where you could comfortably not pursue your father straight away as he's a grown man who can handle himself. As you're pursuing a child in FO4, the same is not true as they're your responsibility and the game makes you feel irresponsible for ignoring it.
Really, I was much happier with the Courier or Dovahkiin who could be literally anyone and could have literally any motivation you liked. Bethesda presumed way too much about the character's motivation in FO4 and I find it incredibly restrictive.
Player determined progression - For me the set up is again a bit wonky as with infinitive levelling again you get this system where over time your characters are going to be convergent. What's the point in having your own progression when everyone is going to be the same in the end anyway? And sure, you can just not invest perks, but that seems like a pretty unsatisfying way to limit yourself (something I'll doubtlessly be doing, but it's a pretty awkward way of dealing with a system that could have been implemented better in the first place).
Factions That Matter - Again I don't this is true, and I don't like how you will always pretty much get roped into a faction if you want to progress. All the factions are unfortunately pretty much the good guys in one form or another with notes of grey, compared to the ballsier factions of NV that did questionable things a large majority of the time (they all want you to eliminate small factions at one point or another who aren't really damaging that much currently, I won't go into details to keep this spoiler free). Further at least the Legion in New Vegas also had questionable methods, and worked as a faction for people who wanted to play a more brutal character.
There's none of that in FO4, making faction choice much more arbitrary that it ever was before. They also never treat you like a merc, and you always get a high up if not leadership position - while some characters may like a factions ideals it would be nice if there was just one that was much more of the side of contracting you rather than you having to buy into what they say (House, anyone?). Beyond any of that NV allowed you to just go Independent - with nothing compelling you to side with any of the factions if you didn't want to. It baffles me, with such a good example set by New Vegas, that the factions are what they are in the game. I even much preferred Skyrim, where you were under no obligation to align yourself with factions that wanted to govern and when you did both the Imperials and Stormcloaks do dubious things like appointing shady Jarls to further their cause, etc.
Overall what bothers me - I think the worst bit of this game is the massive reduction in player agency by giving your character a motivation from the off, making them subscribe to factions to further the game and massively limiting dialogue choices. It transformed what could have been a good story focussed RPG into what amounts to an adventure game, and sure it's a good adventure game but given my expectations going in the FO4 really fell flat and I think it's the weakest of the core games (FO1/2/3/NV). I'm glad I received the game as a christmas gift as if I'd had bought it with my own money my many issues with it really would have made me bitter, as it stands I can currently enjoy it for what it is and not get too bogged down by what I don't like about it.