I see where you're coming from. These rules are really for a more survival based game rather than a definitive role play experience. A bit more like Resident Evil, where enemies carry a real threat and ammo and weapons are not in abundance.
Though, having said that, it works both ways. Lets take your first example, of the character with high intelligence. The vastly increased skill points you would have from high INT special would have to be shared out over other skills once you have maximised your core tag skills (let say Science, Speech and Medicine, for example). This would most likely end up with a character who is excellent at just about everything, which would actually dilute the role play experience you are trying to achieve.
For the second example, rather than focusing on Endurance as the benchmark of physical fitness, lets say a combination of Strength and Agility are instead. By still capping your Endurance (and Intelligence) at 4, you are free to pour points into any other SPECIALs as you like. So if you want a starting 9 in both Strength and Agility, then go right ahead.
Of course, none of this is set in stone and you can adopt whichever rules you like the most. The initial focus on Endurance and Intelligence SPECIALs are mainly due to their huge influence on hit points and skill points - two main factors that overpower the player character.
To be honest, it's not the lack of Skill Points which bothers me (we'll always have enough of those regardless of Intelligence stat), but rather the loss of unique dialogue choices. Even writing this I can see that's a very petty matter, but it all adds to the immersion IMO.
Still, I'm willing to compromise dialogue for an overall more immersive experience. And I advocate your idea on Strength and Agility -- really, the Endurance SPECIAL only affects, what, 10 HP per point? I guess you can assume that the fact you're character's even surviving in the CW is a testament to his endurance.
On a seperate tangent, I'm interested in how one would utilise the Skill Books located in every single [censored] place explorable. Reading the same book over and over makes little sense, so I propose only reading it once, perhaps? Though, the 1 skill point gained would likely prove rather irrelevant, anyway.
Anyway, if I find myself the times between revision and my ever declining social life, I may be interested in giving this is a whirl. If so, I'll be sure to update on noticable progress if you wish.