I'm around 60 hours in the game. I love it so far, but... yeah, we need to add some things and change some things.
1. Let us upgrade more armors. I'm not talking about attachable pieces, but armors like road leather, raider leather etc. What's the point of them, especially on v.hard and survivor mode, if you can't upgrade them? Same goes with full body armors like Kellogg's or Cage/Spike armor. They're so horribly weak and we can't upgrade them and we can't even attach anything to them. So. Stupid.
2. Please, put some kind of a marker on our companions when we look at the map/minimap. It's a pain trying to find them otherwise. Yesterday I spent 10 minutes before I found Piper and then another 10 minutes before I found Deacon. I swear, sometimes companions are glitched and they disappear without a trace.
3. We can place bobbleheads on the special stand, magazines too, but what about food and alcohol? I've built in the sanctuary small, pretty bar, but shelves where alcohol is supposed to be are empty. I've tried to drag bottles manually, but they just keep falling. I know, small thing, but it would be really great to have this option.
4. Give us more options to build things in our settlements. Furniture, walls, decorations etc. I know we can unlock some with magazines, but... give us more!
5. Limit is ridiculous. Only 20 in total? No, just no. Please, change it, Bethesda. You gave us an awesome feature, but yet again, so limited.
6. We need a better system to track our settlers' job. The current one is terrible and I constantly keep guessing who works where.
7. Okay, we need a warning when we accept a quests and it's only for a limited time. Quests like clearing ghouls/mutants for some villages or clearing area for a new beacon. I had no idea that if we ignore them for too long, they will fail. So yeah, warning would be nice. Or at least show us how much time we have left to finish theses quests.
8. It would be really great if we could travel with dogmeat + one companion. Just like in NV. I usually pick Piper or some other "humanoid" companion to have comments during quests, so yeah... dogmeat just sits in the sanctuary all the time.
9. We really must have some kind of tutorial for building the settlement for the first time. We're just thrown in the deep water right at the beginning and we have to guess how to build everything. No tips, no nothing. Honestly, Bethesda. Why would you do it? I constantly see forum topics where people ask how to build this or that. Or how to handle the electricity. Not only here, but on reddit or other sites.
That's all for now. I'll add new suggestion if I think of something new.