Mercurius
Legend
I hear you and have always taken issue with the over-simplicity of the D&D rules, in this regard. I'm not sure there's a way around it, though, without either making it far more complex, or changing it radically.
There was a game that came out in the early 90s called Aria that was focused on "telescopic" role play, where players played entire kingdoms and people within it, that took a different approach to bonuses. If I remember correctly, there were ten or more attributes,and each skill, including combat, had a list of attributes that you could draw from to get bonuses. This allowed you to build whatever type of character you want, to create Oberyn or the Mountain, so to speak, and up with a similarly skilled warrior. In other words, your Sword skill might use bonuses from Dexterity, Agility, and Wits (or whatever the attributes were), because that is the type of swordsman you were (e.g. Oberyn).
The point being, what makes a warrior good at combat is not just how strong they are, archery isn't just about hand-eye coordination, and magic shouldn't just be how smart you are in a IQ sense (a concession to nerdery, I think). All of these activities involve a number of attributes, which can be combined in different ways.
A more realistic approach would be to do away with ability scores and expand the skill list, grouping them into "aptitudes" (or some such), each of which has a natural ("talent") and trained ("skilled") component. so if Sword is a skill within the Combat aptitude, a player would start with a Combat talent bonus and develop their skill through adventuring. Of course that would end up making D&D a different game.
But I digress...
