Fallout 4 is a lot of fun to play, and the open world is great. I've sunk a few days into the game and enjoyed myself for the most part.
However - the main storylines and faction storyline are pretty poor, in my opinion. I hope that Bethesda doesn't look at the review scores from "professional" reviews on the big gaming websites and conclude that they did everything right.
First of all, to repeat a criticism that is becoming a bit of a cliche by now, the main story completely fails to create any emotional connection with the murdered wife or kidnapped son. I never cared about either of them because I didn't know them. Then, when the main character starts emoting about them during certain dialog, it was pretty jarring, because I certaintly wasn't getting misty-eyed.
Second, it seems that Bethesda's idea of weighty choices is deciding which faction(s) the play has to murder wholesale. It's lazy. If the player decides to a "nice guy", he'll find what he is being asked to do pretty abhorrent. This effectively forces the player towards the Minutemen, because they seem to be the only faction that doesn't suffer from extremism. Now you might argue that the extremism of the other factions is intentional, but even extremist organisations realise when they don't have the strength to eliminate the opposition, and act pragmatically, i.e. they are forced to negotiate. There should be some way for the player to influence the course of action(s) taken by the factions, e.g. by refusing to cooperate with something that they need accomplished.
Third, the way the main questline and the faction questlines interact is poor, apparently because they interact so much in ways that the quest logic does not anticipate. For example: in my playthrough, I tried to avoid all-out war between factions, with the result that I advanced some of the faction questlines up to the point of causing hostilities with another faction. After destroying The Institute and basically "finishing" the game, Maxson acted as if I was returning to him with intelligence about the whereabouts of synths in "Battle of Bunker Hill".
Fourth, some of the plot devices are ludicrous. As has been said many times already, it's silly that you become "General" of the Minutemen or get fast-tracked to the rank of Paladin in the BoS. This would never, ever happen in any real-world organisation, not just because of the resentment it would cause, but also because a newcomer simply wouldn't be trusted. The game doesn't have to be all about the player. Given that the player is essentially tasked with a lot of dirty jobs by the various factions, it would have been much better if the game had taken exactly that line instead, e.g. the BoS doesn't allow you to be a member but uses you as a well-paid mercenary, giving you a set of power armor in order to ensure your success. That would be much more in keeping with their ethos and way of operating.
Another ludicrous plot device is the doohick that the player has to build to get into The Institute. True, it's not actually a teleporter (it's supposedly using The Institute's signal), but it's silly that a bunch of wastelanders can build such a thing in a day or two, let alone wrap their heads around the technology it uses. Weren't Bethesda's writers capable of coming up with a more plausible plot device?
Fifth, the game is unmistakeably dumbed down compared to previous installments. Making NPCs unkillable, so that they just sit on the floor for a bit, is lazy game design. In previous Bethesda games, the number of NPCs that were marked as "essential" was fairly limited, but in Fallout 4, it seems that this has been adopted wholesale as the solution to any problem where killing an NPC might break some question or other. This is probably done because NPC AI has zero sense of self-preservation and giving them sufficient AI to not get themselves killed is too much effort. However, if Obsidian (Fallout NV) managed to avoid using this solution everywhere, why can't Bethesda?
Sixth, the perk system, where all of the ranks of a perks are gated by a particular SPECIAL value and/or level: I've tried to approach this with an open mind, but I have come to the conclusion that I don't much like it. The new perk system has obviously been designed so they all fit nearly onto the perk chart. It would be far more logical, in the context of the game world, if (for example) the ranks of "Strong Back" were gated by different SPECIAL values as well as by level. But then the nice neat perk chart would not have been possible. This seems like a case of style over substance.
This thread on Reddit sums up a lot of frustrations with the story and quests quite nicely:
https://www.reddit.com/r/Fallout/comments/3stzg9/fallout_4_story_svcks_there_i_said_it/
Despite these faults, Fallout 4 is a cool game and deserves most of its praise, but I really do hope that Bethesda listens to the criticism of its flaws, which have been entirely overlooked by most "professional" reviews.