I think my only real big complaint is that the game is a bit too over populated with enemies and loot (makes encountering both too common to feel precious)

This is made worse by the fact that the enemy AI is terrible. They either just sprint towards you or stand out in the open a few meters away. Then I just melt through them with all my easily found top-tier weapons and ammo (whilst my companions soak up most of the attacks). Or when a disguise fails in a restricted areas and you're spotted, you can just use the most basic speech checks to evade any trouble. The game feels so easy on the default difficulty. And all the higher difficulties do is up the damage enemies inflict. The enemy variety is also lackluster.

Another gripe is that, excluding that first big decision you have to make, none of the in-world decisions feel that impactful. This is amplified by the fact that there always seems to be a way that you can have your cake and eat it too by pleasing all sides of issue. Don't get me wrong, that's cool in some scenarios. But I'm 15 hours into the game and have made multiple world-effecting decisions, yet all the opposing factions still like me. That seems a bit odd.

Despite having spewed all that negativity, I am overall enjoying the game though. As you say, the writing is generally fantastic and the world it creates is enough to elevate the game. I especially love all the subtle interactions that happen between the characters. The gunplay, whilst not being anything to write home about, is also satisfying.