First off, I appreciate your props and like some ideas you have in your massive theory (The Jack and Nory One). Some of your thoughts are interesting and certainly challenge the mind.
But, and this is a big BUT, I seriously doubt the logic of many of your perk positions.
1: Tell me, why would you be capable of learning and physically capable of wielding a bat before your own fists? This is one of the most perplexing elements of your setup.
2: As they have made a point of having a huge focus, in the thread of mine you link, I have suggested a specific scene on the Perk Chart where a perception perk (Heave, Ho!) is pitching to a strength perk (Little Leaguer), both at the 2nd level.
3: Why would Ninja, a martial art specifically based in stealth and agility, be in strength? It would only make sense in Agility, the domain of Sneak (what Agility effects). Also, you don't see the Shuriken in the tenth perk in the Agility Perk column?
4: Why would any reasonable game designer gate 20-30% (probably) of the weapons (Plasma Pistols, Plasma Rifles, Laser Pistols, Laser Rifles, Gatling Lasers, Cryo lasers, and flamers) at such a high stat? I honestly feel that most major 'skills' and crafting abilities will be 6 and below. Intelligence 9 is likely very powerful, but very limited, like the Educated I suggest in my thread. I feel Science is 6, mostly because it looks much more like it, as the energy weapon is much more level with the head (like it is in the E3 demo), where as the "energy weapons" (see cap) is way higher in the rank 9 perk.
5: Chemist and Medicine/First Aid are likely combined in their effects. Also, Fast metabolism is likely wrapped up in the medicine skill.
6: Attack Dog is likely a perk that boosts your companions effectiveness in combat.
7: I believe that most of the perks in the relevant stat predominantly relate to that stat and leave that domain very rarely, if at all. So, I don't see how an intelligence perk is going to affect your shot, as it seems that Agility and Perception contain those elements.
There may be more criticisms, but these are the biggest ones I notice right off the bat. Like I said, I appreciate your props, but I have some serious doubts on your deductions here.