So what would you do with the fifth bonus? Or the sixth?
And if Athletics is divided into subsets for the bonus, is it also divided for the penalties? That is, are we back to being able to distribute penalties into places where they won't come into play?
Note that these same questions come up for all other ability bonuses and penalties as well.
By condensing down the skill sets, and at the same time forcing a limited distribution of ability modifiers, you run into the problem we're seeing: You can't use all the bonuses and/or penalties. But if you don't limit the possible places to share them out then it becomes possible to hide our weaknesses so they don't really come into play.
Plan C would seem to be grouping skills, like Athletics, and once they're invested then allow sub-specialties. This runs 180 degrees out of synch with your goal of "flattening" the system (i.e. dumbing it down.)
Have you considered a return to 1e, where there were no skills, and ability mods only came in for exceptional abilities, usually 16+, and were class specific? (I.e. only Fighters could roll on the "Extraordinary Strength" chart.) It was already "flatttened", everything done through skills and feats were done as class abilities or "Non-combat proficiencies"?
Note that by subsuming feats into class abilities, as you've suggested, you sabotage your own stated goal of having two characters of the same race/class/ability be completely different. You are removing choices, which was 3e's strong point.
I'm a system's analyst by trade, so it's kind of natural for me to analyze proposed changes to a system, be it an office system, computer system, manufacturing system or a game system.
I once wrote a supers game system, and later tried to retrofit it on the D20 model. It didn't work because super heroes have super stats, and they overwhelm anything resembling balance in the D20 skill system. That's sort of the battle you're fighting here, on a smaller scale. You don't like the fact that a gifted athlete can be good at many sports, that a gifted scholar can be knowledgable on many subjects, that a wise and insightful person can display good sense in a lot of areas, that a friendly and personable individual can... well, you get the picture. But the fact is, an intelligent person doesn't stop being intelligent when the subject changes. A man who can lift his own weight over his head doesn't suddenly become a weakling when it comes to lifting his own weight by climbing a rope.
And though I hate to argue reality in the realm of fantasy games, that's the way things work in the real world. Most college athletes have several choices as to which sport to compete in. Football players often wrestle in the off season, and they lift weights and run to train for either one. Some play baseball as well (if they still have the knees for it), and the taller ones play at basketball as well.
You don't have to be Rain Man to be good at math, and being good at math doesn't preclude also being good at history, social science, etc. In short, 4.0 gpa students exist (My wife graduated UCLA Cum Laude, for example). In your proposed skill/ability system they either all become 4.0 students because you've lumped all the academic/knowledge skills into one (ala Athletics), or none of them do because there are too many places to put ability/skill numbers.
And the simple fact is there there are varying degrees of Strength. +/-1 max to Lifting from Strength? Everyone's either Joe Average, Willy Weakling, or an Olympic class weight lifter, with nothing in between. Every competition ends in a tie because everyone competing has exactly the same capacity (+ to Lift). Is that how "flat" you want things? It's what you're building, after all.
(DC Heroes had that problem, sort of: Every point doubled ability, so Clark Kent was either supposed to be twice as strong as Lois Lane, or exactly the same. So was Jimmy Olsen. No real gradations. Oh yeah, Joker was twice as Intelligent as Batman,but Batman could outrun a race horse, two to one.)