Why hasn't anyone brought up ratchet and clank?
I know, I know, not really an rpg, but look at how the player growth was largely based in weapon growth. As you used a weapon more, it got stronger, did more effects or even evolved into a new weapon. If you look at that as instead of the weapons growing and more like a growth of ratchet getting better at using the weapon (for guns, this doesn't make much logical sense, but for melee, bows or magic it does), then it is sort of the system being asked for.
Rather then numbers signifying how strong someone is and having that be part of bonuses applied to use of weapons or magic, I think what is being asked here is streamlining that to a more similar system as mentioned above. Rather then arbitrary measures of strength or intelligence, simply have character growth in those regards tied into what they would support anyways and have growth stem out of use of the weapons or skills.
This also could make sense as swinging a heavy weapon is likely to make you stronger as you get ore accustom to it. You will develop callouses and muscle memory the more you use a bow or whatever. And you will be able to retain knowledge, and I suppose spells, the more immersed you are in the knowledge.
There is a certain logic in the more you use something, the better you get at it. When it comes to active skills, such as combat, spell casting and the like, this should be very easy to implement. When it comes to aspects such as health or stamina, a little less so but not impossible. It could be based in damage received, or if you don't want that abused, you could have it ties to equipment, relics, specific items that increase it by whatever percentage... lots of options. Hell, you could keep it the same throughout the game, so that it better represents how hard it is to make yourself better then an arrow to the face.
bitter end -catcha, you have been rather dark of late