Well ultimately, you have to decide if trivialising powerful monster races is a negative thing, and if it harms the setting, I totally agree that it does. Having fewer, much more challenging creatures like Aboleths, Pit Fiends, Beholders, even Drow, is just better design and implementation than having large numbers of them swarm you and be trivial to dispatch. Certain monsters and races are entirely designed to be horde like and relatively none threatening (in the broader sense), like bats, goblins, wolves, undead in general. Using a nebulous Non satisfactory explanation of "The Dark Powers made them this way" is just lazy.
Calling it lazy is unfair.
The problem is that we are in a game (not PnP) more than 20 years old, famous for having lots os things hardcoded. In PnP you can easily create new monsters as your imagination demands. Were the game open source and easy to code it would be possible too. You could simply say they are Devil Johns, a mockery of the pit fiends bred in Perfidus and ok. You caould call the Aboleth the Andrew, the psychic Octopus or whatever.
The question to be balanced is how much development work will it takes to re-skin those monsters to something non-immersion breaker and it this amount of work would be more appreciated anywhere.
Your completely correct, re-skinning would be a fanciful idea, and no one has seriously suggested that anyone should even try it, and certainly no one is suggesting coding or changing how the game functions, that seems to be a red herring that you're throwing into the discussion. It's all about utilising the resources in the toolset, which are absolutely phenomenal by the way, the different combinations of creatures, classes, equipment, skills, VSFX, portraits, voice sets, means you could easily create hundreds of thousands of combinations of content, and I'm only talking about creatures here, not areas, lighting, traps, and scripts.
Regards "Andrew the Psychic Octopus", you're actually misrepresenting a tool that developers have to create a unique and meaningful encounter. Picture an Aboleth Dungeon, at the far end of the dungeon is the end encounter, an Aboleth. You place various creatures that are suitable for the dungeon, creatures that Aboleths would conceivably dominate and use in there schemes, and would encounter, the players fight there way through it to get to the end point of the dungeon and what do you find...a creature called "Aboleth", which is not unreasonable, but is that the best implementation of the creature? No, certainly not. You can immediately improve the encounter by making a small change by giving it a name, "Xu'garth the adolescent Aboleth".
With that one small change, you have shown that actually, this top tier monster, who has the potential to dominate and enslave humanoids, and mastermind organised groups of townsfolk, influential organisations, religious cults, noble families, royal courts, wasn't just a random no name NPC sitting at the end of a dungeon waiting to be vanquished, it was actually just a adolescent. You could even go one step further, and at the end of the encounter the "real" Aboleth was actually just projecting an illusion via the enslaved elven enchantress, and the real "Xu'garth the adolescent Aboleth" swims away while the party is trapped behind a immovable barrier that this genius creature installed so that it could make it's escape.
It's all about how you use what's available.
