1 - CRAFTABLE AMMO, i know it's not hard to find it or buy it just it would be a nice little convenience that makes sense to have.
2 - Add some more CRAZY and fun legendary drop weapons, go nuts with it however make the legendary mobs MUCH MUCH harder to kill (i feel very underwhelmed by them) and make them a little bit rarer.
3 - Deniable quests, I hate having the 2 constant minutemen quests in my pip-boy... My OCD is kicking in there.
4 - Make it so mobs constantly scale with your level, once you reach level 30 it feels like no matter what difficulty you're on that they just wither away when you blink at them.
5 - PLEASE get rid of the "My Mods" tab on the Pip-Boy and just make it so the mods go onto the weapon (They should never have had their own tab, it's silly) and in doing so will make it much cleaner. I hate having to scroll through that menu to get rid of mods i am not currently using because I sold that weapon or whatever and if i don't they use weight up. (when you have used and modded many weapons that 0.5 weight adds up).
6 - Easy to change FOV, i'd like to not mess with .ini files if possible and just have like a slider.
7 - Also related to FOV (when increasing above default) some screens don't scale up for example when in the power armour with a nice 110 FOV, you have the power armour HUD and then some on either side (it just looks ugly).
8 - Obviously something that Skyrim suffered from HORRIBLE INVENTORY SYSTEM, please bring something out that adds a "search" function or adds more organization options to it, it's just horrible to scroll through so many items just to find a specific item.
9 - Make it so i know when i'm interacting with a NPC i know what i'm going to say. "Sarcastic" is not very in depth and doesn't have any context to it.
10 - MORE CUSTOMIZATION, Don't get me wrong Fallout 4 already has done a fantastic job with it however it can be taken even further! Make it so i can wear the "Silver Shroud" armour with some metal chest plate and raider leather right arm and whatever.
There are PLENTY of mod ideas there i have many more but those are just the ones i want to see the most!
- EDIT -
I can't believe i missed this but please please please please ASAP get a mod to fix all of these little stupid silly bugs!