Please feel free to add to this.
A couple of quick things I've noticed that- if Bathesda doesn't fix, I certainly hope the modding community will..
For starters- and- speaking abstractly- dear GOD work needs to be done with structures snapping to each other (walls to floors, etc...). Building things is sort of a pain in the ass right now. A terrain leveling tool also would be handy.
1. FULLY DEMOLISH/REMOVE: For the love of Pete, please let us demolish all of the structures within a settlement. I don't want the houses that are there. Keep the foundation plots (if you must), but, let us tear down all of the buildings / remove all of the plants/bushes.
2. STORING ITEMS: It took me far too long to realize that when you "store" an item in a settlement, it doesn't go to your workbench. The game just randomly plops that item down somewhere else in the settlement. I was like: Why the hell does Sanctuary have so many sofas?. If I store something, please place it in the workbench so I can clean up the settlement.
3. ADDITIONAL SETTLEMENTS: Please give us the option to relocate settlers between settlements. I hate that I have four settlements with three people each. Ideally, I'd like to get a new settlement, drop a turret and a recruitment becon and then set a waypoint so taht those new settlers show up in Sanctuary (one settlement w/ forty people instead of ten settlements with four people). Then, if and when we want to expand into a new settlement and build it up for some reason, we can.
4. SETTLMENT UI: Please add a way to better understand what is happening with the people in our settlement with regards to who is assigned to what task. Even something as simple as the NPC's name changing from, say:
Settler = unassigned
Settlement Guard = assigned to guard post
Farmer = assigned to tending crops
Caravan Leader = assigned to supply route
It's such a pain in the ass to try and set something only to have your food supply tank.