One area where I think Bethesda games could greatly improve upon are the generic NPCs, enemies, groups, and factions. You'll be exploring an area, discovering a new location, only to learn it's another place with filler enemies. In Skyrim it was usually Draughr or bandits; in Fallout 4 the most common one being Raiders. It can really start pulling you out of the experience, and I feel negatively affects replayability. Even giving these generic characters random names can make a big difference; ignoring the fact that your character wouldn't know everyone's name. Killing Drego Wilhelm, bandit, has the potential to be a lot more engaging then just 'bandit'.
I feel there is a great solution to this, and Bethesda already has a lot of the concepts and foundations with the radiant system and legendary enemies and equipment. They have radiant quests and radiant AI. Now they should create radiant NPCs, enemies, groups, and factions. A great example of this is Shadow of Mordor's Nemeses system. For those unfamiliar with Nemesis, it's a dynamic system that generates unique, named enemies for each playthrough with their own unique visuals, traits, abilities, etc that rise or fall in their social structure as the game progresses independently of your character (but you can definitely influence them heavily depending on your actions).
Bethesda would of course design their own system, but with something similar to the above it would create dynamic NPCs, enemies, groups, and factions that are unique to your playthrough with their own motivations, behaviors, stats, appearance, combat styles, loot, etc. For example, one enemy could be focused on building up a stronghold, an NPC could try to slowly expand their business and influence, another could be a roaming band that pillages and moves on, another a small band of murders or assassins. All of these actions could happen independently from the player, but could also be influenced by your actions.
This would create a much more diverse, breathing world. In one playthrough a location could be deserted; in another, it could be a fortified stronghold or a small trading hub. You clear an area, and come back later to a village being built by a new group moving in. This would also give incentive for players to revisit locations as they would change over time. This would also facilitate more random encounters between various factions and groups fighting or interacting with each another such as unique alliances or rivalries.
These NPCs, enemies, groups, and factions could also react to the player in unique ways. One leader may seek you out deliberately; a faction could be cowardly and run away from you after you've done certain feats, or flee when a certain number of their followers are killed. They could be friendly to the player. The potential and variation could be endless. This system would not take the place of well developed, "permanent" characters, quests, factions, etc. that are there for every playthrough. It could even enhance these elements. This could be developed well beyond the shower thought I have here.