There is one major disadvantage to your way of thinking. It is unlikely that in most cases we will encounter a given creature more than once during the game. Of course, this does not apply to enemies that are related to the plot, such as goblins or standard humanoids.
Of course, there is also a chance that we will meet opponents with the same model later in the game, but they will most likely have different stats anyway.
It is also not stated that a given creature cannot differ from another of the same type (like minotaurs)
I don't think it's fair to ignore "enemies that are related to the plot, such as goblins or standard humanoids," as these enemies will be in a larger percentage of fights.
But even if we do face most enemies only once, a partial solution is to allow additional nature/arcana checks after killing each enemy. As long as there are multiple enemies of that type in the fight (pretty likely, unless it's a boss-type enemy) then as the fight progresses you'll learn more about how to better kill each enemy.
I'm not sure where the line would be drawn between same creatures of different classes/abilities (i.e., a human rogue will obviously have different stats/AC than a human Paladin)...lumping all humans under a single check/bestiary entry is a bit unrealistic, but requiring a check for every human, however slightly different, would obviously be too much. This depends on the variety of enemies in BG3, which we can't know without having played through Acts 2+.
