First and foremost I must state that despite many claims to the contrary, Fallout 4 is not a 'bad' game. Taken in comparison to FO3 and NV, it is the lesser of the group, but in a vacuum, it's actually pretty good. One thing it also suffers from is excess hype. Bethesda did too good a job building anticipation for the game, and it backfired a bit. People expected too much, based on the hype, and it didn't live up to it.
So, on to the lesson.
What Bethesda did right:
They built a large true open world with a diverse cast of characters and lots to explore. The world is so large in fact that there are entire sections not touched by any of the storyline or miscellaneous quests.
The NPCs are engaging and make sense in the setting (mostly) and the existing towns all fit nicely together.
The equipment and weapon customization system is more than adequately robust, and due to the relative ease of modding FO4, it has been expanded greatly by the community.
The main storyline and quest tree is well structured and sufficiently cohesive without being too linear, and I personally appreciate the option to skip some entire parts of it if those parts don't fit the character or playstyle you're doing on a particular run.
The miscellaneous quests all feel right at home, whether branching off the main questline, or completely unrelated, they all feel like they belong in the world they're set in.
The settlement system is a neat idea, sourced from a mod for FO3 and NV, but expanded well beyond the scope of the original, and allows for a good deal of creativity.
All of this put together makes for a pretty good game, it's fun to play through, has a good deal of emotional depth, and allows for a great deal of freedom when you do certain things. But the shortcomings of the game must be addressed, as they are also numerous, and have seemed to overshadow the good.
What Bethesda did wrong:
The voiced protagonist was a neat idea, but not well suited to the kind of gameplay we expect from a Bethesda open world game. A great many of the 4-option dialogue choices were essentially meaningless in context, and more significantly the inflection of the voices left alot to be desired if you wanted to play as someone who lived outside the normal emotional range. Whether you were playing a living saint or a sadistic serial killer, you sounded the same. Furthermore the lack of an escalation tree for karmic level meant that even the worst character you could imagine could suddenly come out sounding like a saint in the conversation.
The backstory is much too detailed and complete. For the sake of narrative, I realize that they had to establish motivation, but well, there's a reason Skyrim is going to be re-released for the next few decades. The real treat of an open world RPG is that you get to create your character to be whomever you wish. The more you know about the character *before* the game starts, the less control you have in that regard. That's why FONV is so superior to FO3, and by extension to FO4. You start out as 'the Courier'. Nothing more and nothing less. There's no pining for the world you once knew, the family you've lost, or not lost, who knows, not important. And that's exactly the point here.
The settlement system is kind of a mess. Despite it 'just working', it quickly becomes a chore to build whole settlements, and in some areas there are things that you just cannot do without console commands. There's a big house in Jamaica Plains that is fully inside the build area that you can't use, can't remove, can only build on top of in certain areas, and doesn't make any sense even being there. In one of the smallest build areas. Fortunately there are now several mods that balance out the entire crafting system, and add quite a lot of logic to the settlement system in particular. The next game should include a great deal of this new functionality. Putting that aside, making the settlement system an integral part of the main quest line was a foolish decision. There are whole sections that you cannot do properly without building up Sanctuary and dealing with Preston Garvey. In future the settlement system needs to be completely optional.
There's no substitute for hard work, except free Power Armour. In previous games the ability to use PA was something to be earned, and while I wasn't happy with how far along in the game you had to get before someone would train you with it, it did feel appropriately 'earned'. In FO4 you of course can go ahead and get a suit of it in the first 10 minutes of actual gameplay (if you skip right past Sanctuary and Red Rocket). The mechanics and combat in PA feel appropriately badass, but it doesn't make logical sense that you can just walk up and get a set that early. If you're playing a male character, with military history, it at least makes sense that you can pilot the thing, but if you're the lawyer wife... Anyway, in the future PA needs to be taken more seriously as a piece of equipment to be earned.
That concludes the important recommendations that I, an overanalysis nut, hope that Bethesda and/or whoever is making the next game read and take seriously.