This is a compilation of all the improvements I'd like to see in Fallout 4, after 275+ hours of play (on Survival, if that's relevant). I'm focusing mostly on "easy" fixes and refactoring, but also mentioning some bigger concepts:

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Companion Fixes:

• We need a "Command" function for Mama Murphy in build mode (Allowing us to reposition her chair without having to "kill" her).
  
• Cait's mission won't start after she asks you to detoxify her. I think this may be related to exiting dialogue and going into combat.
  
• Companions that haven't yet romanced you, keeps interrupting you with their "final romance dialogue". This can be really annoying at times. You should be the one who starts the dialogue, and it should be (arguably) impossible to romance them once you've already romanced someone else. (I.e. they should no longer interrupt you). I've romanced most of my companions and tucked them away at Red Rocket Truck Stop, as a workaround.

Scrapping Improvements:

• Scrapping is somewhat underwhelming. Settlements should have an extended "scrap area / perimeter" in which you can scrap items (but not build). With so many trees in this game, I find it strange that Wood is so hard to come by (because you need so much of it, especially for making a bustling settlement at several workshops. Alternately, Shipment of Wood should perhaps be sold by more people. In fact, I don't recall ever finding Shipment of Wood in any stores at all.
  
• We should be able to scrap junk that we've stored inside the Workshop inventory, either individually and/or through a "S) Scrap all Junk" command (that, if necessary on the consoles due to the "extra-button problem", could replace the "Store all Junk" whenever the Workshop Inventory is in focus),
  
• Scrapping the rubble at The Castle (in order to reach the underground tunnel), is brilliant game design. We need more of this, where scrapping reveals access, alternate routes, secrets and more. For instance, the beached barge at Spectacle Island has a lot of containers filled with scrappable boxes. Behind these boxes, there should've been a secret safe or similar containing, perhaps, a unique weapon or otherwise. Sadly, I've yet to find any such secret (anywhere in the game).
  
• In the future, perhaps in a DLC, there should be some endgame ability to scrap any items anywhere in the world.
  This could be achieved by using a "Dematerializer" or "Translocator Gun" or w/e. The reload button changes the settlement that the scrap is "beamed away" to (or, alternately, the scrap just ends up in your inventory, perhaps as "Shipment of X" which you cannot sell until you've redeemed it as materials in a settlement). The "gun" uses a specialized Fusion Core item (found perhaps in the Glow) as its build requirement, as well as Science IV and Scrapper III (rank added for this feature). Alternately, it could require Nerd Rage I because, well... you get my point.
  
• Shipments should be "Shipment of X (amount)", instead of "Shipment of X - 25". E.g. "Shipment of Lead (25)", treating the shipment as 1 unit of material, thus allowing us to specify how big our shipment should be. The word "Shipment" is just an abstraction, anyways. Keep in mind that this suggestion relates to the aforementioned Dematerializer feature in which you can acquire Shipment of [material] through scrapping and not just in stores.
  
• Whenever you invest in a store, we should maybe get access to increased quantities of junk and Shipments - e.g. same items but higher quantities.

Settlement / Building Improvements:

• Settlement distress calls (Minutemen radiant quests) are too frequent / distracting, once you got enough settlements unlocked. This needs to be reduced and/or possible to switch off entirely, e.g. by switching off the beacon at The Castle (which I did, to see if it worked - which it didn't). This may not be an issue though, with 100+ Defense. I've yet to confirm if these quests will still fail if you don't visit to help.
  
• The Benevolent Leader achievement (100% Happiness in a Large Settlement) shouldn't be this hard to get. In fact, it seems bugged - 100% size, all stores/crafting, max settlers, 100-150+ defense, 20+ food, 40+ water, 20+ beds, lots of decorations and chairs, and still my settlement fluctuates between 80-85%. I know about the Townbell / Waiting exploit to get 100% happiness, but that isn't a very good "intended feature", IMO.
  
• Containers:
  I was disappointed to learn that many containers in the game aren't buildable in workshops - Ammo Boxes, First Aid Boxes, Chem Boxes, upright Lockers and similar to help flesh out your base and give it character. But also things like bathroom Mirrors, Institute-style containers and other items that you use to decorate your home. I'm hoping to see major improvements on what you can build at workshops, in content patches as well as future DLCs.
  
• Static version of placed junk:
  It's possible to drop junk and then grab it in build mode, for a more controlled placement. The problem, however, is that the item still interacts with physics. E.g. a typewriter that you place on a desk, will often end up on the floor underneath in, when you leave and then return later (presumably due to its interaction with the desk's surface) Same is true for many other objects, some of which "explode" when you bump into them.
  
  Solution: As long as items are placed in build mode, they should be static items with a fixed position. Game physics may not be easy to change, but making items static should be a doable workaround. They're only static as long as they're placed in build mode and, if you then pick them up and drop them normally, they revert back to being dynamic.
  
• Important "Floor / Roof" objects (to remove some gaps):
  We need a "Shack Upper Floor - Small" that removes certain gaps between walls and upper floors, whenever you use the smaller floors and the stairs in your designs. Currently, only "Shack Upper Floor" (large floor size) exists. In addition, "Shack Foundation" (concrete or wooden poles) should not be a floor element - or - they should have additional versions that snap to the underside of existing floor elements, similar to how flat roof elements work. Right now, the shack foundations are incompatible (snapwise) with prefabs and floor elements. They'll snap adjacent to the floors, but not underneath them. It should be the other way around.
  
• Removing corpses should also be possible in build mode. Sometimes, a dead (named) settler, previous inhabitants or monsters (like the Mirelurk Queen at Murkwater Construction Site) won't despawn over time. So we should have the ability to manually "Scrap" or "Remove" corpses.

Combat / Equipment / Inventory Fixes:

• Better mods for early- to midgame weapons:
  Lategame, you can get Ballistic Weave for clothing. But weapons tend to get obsolete, especially on Survival (where bullet sponging occurs quite frequently). So you're forced to use weapons like the Gauss Rifle, Gatling Laser or legendary Plasma and Laser weapons (with extra damage). .50 cal Sniper Rifles with Rifleman V barely works. But at this point in the game, we're done with "weapon progression". As such, we should have some way to enhance earlier weaponry with high-tech equipment that requires Gun Nut 4 and makes them relevant for late game. And whatever happened to the BB Gun, Bethesda!?!?!? Aaaargh *shakes fist*
  
• When reloading Gatling Lasers, the old Fusion Core will sit in your inventory as it's own item (stacking only with cores that have the exact same charge amount). This means that you could, in theory, have 100 lines of "Fusion Core" cluttering up your inventory. But just having 30 lines of "Fusion Core" is annoying enough. Please fix this, e.g. by automatically, or letting us manually, combine a fusion core with another to transfer charge. I.e. Fusion Core (45) + Fusion Core (30) becomes a Fusion Core with 75 charge. Then that one + Fusion Core (15) becomes a new core with 90 charge, and so on.
  
• Keys and passcards in Fallout 4 are a bit annoying. In Skyrim, keys were treated like any other items that you could place inside containers. So why regress from this in Fallout 4? Also, if you want Keys to be essential and undroppable, then at least put them in a separate section of the inventory, called "Access" or just "Keys". Every time I go through my "Misc." list to check up on notes and holotapes, I'm seeing keys... keys everywhere. Why did it have to be keys? I've had it with these damn keys on this damn Pipboy! Keys, Bethesda - do you speak it?!?!