1. Defending settlements.
Seriously, if you put the effort in to building your settlements any you have over 500 defense aimed at 1 or 2 choke points you should not have to show up to successfully defend your settlement. I show up and my defense hits the enemy so hard before I even ready my weapon that their corpses despawn. Yet everything is destroyed if I either don't show up or an enemy gets so scared of my base defenses that they actually run away and hide so I fail defending the settlement.
Plus with all the defense that the settlements have, why, why, why do settlers insist on running outside the base to attack raiders.
2. Companion weapons.
Base companion weapons have unlimited ammo and settlers have unlimited reloads as long as you equip them with ammo. We should at the very least have unlimited ammo with companions using their base ammo. At least you could upgrade Strong, Cait, etc with a decent upgraded weapon that they won't burn through thousands of rounds of ammo in one encounter.
3. Lack of a diplomatic ending.
The 4 factions really are not far apart on their goals. I would love to be able to bring all sides to at least a fragile cease fire so they can open a dialog and explore their options.
Edit: Adding my response to a question about #3.